Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c110' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/8069522-fedora-rawhide-x86_64 --chroot fedora-rawhide-x86_64


Version: 0.73
PID: 6746
Logging PID: 6747
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': False,
 'build_id': 8069522,
 'buildroot_pkgs': [],
 'chroot': 'fedora-rawhide-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '8b31c3f07cd286923ac6314cb840a923ea666f30',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/bowtie2',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'bowtie2',
 'package_version': '2.5.1-5',
 'project_dirname': 'zlib-ng-rebase-fedora',
 'project_name': 'zlib-ng-rebase-fedora',
 'project_owner': 'ljavorsk',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/ljavorsk/zlib-ng-rebase-fedora/fedora-rawhide-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None}],
 'sandbox': 'ljavorsk/zlib-ng-rebase-fedora--ljavorsk',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'submitter': 'ljavorsk',
 'tags': [],
 'task_id': '8069522-fedora-rawhide-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/bowtie2 /var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2 --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/ljavorsk/zlib-ng-rebase-fedora/bowtie2', '/var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2'...

Running: git checkout 8b31c3f07cd286923ac6314cb840a923ea666f30 --

cmd: ['git', 'checkout', '8b31c3f07cd286923ac6314cb840a923ea666f30', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2
rc: 0
stdout: 
stderr: Note: switching to '8b31c3f07cd286923ac6314cb840a923ea666f30'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 8b31c3f automatic import of bowtie2

Running: copr-distgit-client sources
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2
rc: 0
stdout: 
stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD
INFO: Reading stdout from command: git rev-parse HEAD
INFO: Reading sources specification file: sources
INFO: Downloading v2.5.1.tar.gz
INFO: Reading stdout from command: curl --help all
INFO: Calling: curl -H Pragma: -o v2.5.1.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/ljavorsk/zlib-ng-rebase-fedora/bowtie2/v2.5.1.tar.gz/md5/16caf86d239b176a4f367c9f63bd99c0/v2.5.1.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 10.1M  100 10.1M    0     0  25.0M      0 --:--:-- --:--:-- --:--:-- 25.0M
INFO: Reading stdout from command: md5sum v2.5.1.tar.gz

Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2/bowtie2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727276439.052334 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2/bowtie2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1727276439.052334 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2/bowtie2.spec)  Config(fedora-rawhide-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.6
INFO: Mock Version: 5.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1727276439.052334/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:rawhide
INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide
INFO: Copy content of container registry.fedoraproject.org/fedora:rawhide to /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1727276439.052334/root
INFO: Checking that registry.fedoraproject.org/fedora:rawhide image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:rawhide with podman image mount
INFO: image registry.fedoraproject.org/fedora:rawhide as /var/lib/containers/storage/overlay/f4f5d9a7fcdfd40ccef681894024d8d186d1adc68bea7d28f55eb3985cfe2962/merged
INFO: umounting image registry.fedoraproject.org/fedora:rawhide (/var/lib/containers/storage/overlay/f4f5d9a7fcdfd40ccef681894024d8d186d1adc68bea7d28f55eb3985cfe2962/merged) with podman image umount
INFO: Package manager dnf5 detected and used (fallback)
INFO: Not updating bootstrap chroot, bootstrap_image_ready=True
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1727276439.052334/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf5 detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.94-1.fc42.x86_64
  rpm-sequoia-1.7.0-2.fc41.x86_64
  dnf5-5.2.6.2-1.fc42.x86_64
  dnf5-plugins-5.2.6.2-1.fc42.x86_64
Start: installing minimal buildroot with dnf5
Updating and loading repositories:
 fedora                                 100% |  13.5 MiB/s |  21.8 MiB |  00m02s
 Copr repository                        100% |   5.3 MiB/s | 568.5 KiB |  00m00s
Repositories loaded.
Package                            Arch   Version                    Repository      Size
Installing group/module packages:
 bash                              x86_64 5.2.32-2.fc42              fedora       8.2 MiB
 bzip2                             x86_64 1.0.8-19.fc41              fedora      95.7 KiB
 coreutils                         x86_64 9.5-9.fc42                 fedora       5.7 MiB
 cpio                              x86_64 2.15-2.fc41                fedora       1.1 MiB
 diffutils                         x86_64 3.10-8.fc41                fedora       1.6 MiB
 fedora-release-common             noarch 42-0.3                     fedora      19.4 KiB
 findutils                         x86_64 1:4.10.0-4.fc41            fedora       1.8 MiB
 gawk                              x86_64 5.3.0-4.fc41               fedora       1.7 MiB
 glibc-minimal-langpack            x86_64 2.40.9000-1.fc42           fedora       0.0   B
 grep                              x86_64 3.11-9.fc41                fedora       1.0 MiB
 gzip                              x86_64 1.13-2.fc41                fedora     389.0 KiB
 info                              x86_64 7.1.1-1.fc42               fedora     361.9 KiB
 patch                             x86_64 2.7.6-25.fc41              fedora     266.7 KiB
 redhat-rpm-config                 noarch 295-1.fc42                 fedora     186.6 KiB
 rpm-build                         x86_64 4.19.94-1.fc42             fedora     194.3 KiB
 sed                               x86_64 4.9-3.fc41                 fedora     861.5 KiB
 shadow-utils                      x86_64 2:4.16.0-4.fc42            fedora       4.1 MiB
 tar                               x86_64 2:1.35-4.fc41              fedora       2.9 MiB
 unzip                             x86_64 6.0-64.fc41                fedora     386.8 KiB
 util-linux                        x86_64 2.40.2-8.fc42              fedora       3.7 MiB
 which                             x86_64 2.21-42.fc41               fedora      80.2 KiB
 xz                                x86_64 1:5.6.2-2.fc41             fedora       1.2 MiB
Installing dependencies:
 add-determinism                   x86_64 0.3.6-1.fc41               fedora       2.2 MiB
 alternatives                      x86_64 1.30-1.fc41                fedora      66.3 KiB
 ansible-srpm-macros               noarch 1-16.fc41                  fedora      35.7 KiB
 audit-libs                        x86_64 4.0.2-1.fc41               fedora     331.3 KiB
 authselect                        x86_64 1.5.0-7.fc41               fedora     153.5 KiB
 authselect-libs                   x86_64 1.5.0-7.fc41               fedora     818.3 KiB
 basesystem                        noarch 11-21.fc41                 fedora       0.0   B
 binutils                          x86_64 2.43.50-1.fc42             copr_base   27.5 MiB
 build-reproducibility-srpm-macros noarch 0.3.6-1.fc41               fedora     735.0   B
 bzip2-libs                        x86_64 1.0.8-19.fc41              fedora      80.7 KiB
 ca-certificates                   noarch 2024.2.69_v8.0.401-1.fc42  fedora       2.6 MiB
 coreutils-common                  x86_64 9.5-9.fc42                 fedora      11.2 MiB
 cracklib                          x86_64 2.9.11-6.fc41              fedora     238.9 KiB
 crypto-policies                   noarch 20240828-1.git5f66e81.fc42 fedora     136.9 KiB
 curl                              x86_64 8.10.1-1.fc42              fedora     453.3 KiB
 cyrus-sasl-lib                    x86_64 2.1.28-27.fc41             fedora       2.3 MiB
 debugedit                         x86_64 5.0-17.fc41                fedora     199.3 KiB
 dwz                               x86_64 0.15-7.fc41                fedora     290.9 KiB
 ed                                x86_64 1.20.2-2.fc41              fedora     146.9 KiB
 efi-srpm-macros                   noarch 5-12.fc41                  fedora      40.1 KiB
 elfutils                          x86_64 0.191-8.fc41               fedora       2.6 MiB
 elfutils-debuginfod-client        x86_64 0.191-8.fc41               fedora      64.9 KiB
 elfutils-default-yama-scope       noarch 0.191-8.fc41               fedora       1.8 KiB
 elfutils-libelf                   x86_64 0.191-8.fc41               fedora       1.2 MiB
 elfutils-libs                     x86_64 0.191-8.fc41               fedora     646.2 KiB
 fedora-gpg-keys                   noarch 42-0.2                     fedora     126.4 KiB
 fedora-release                    noarch 42-0.3                     fedora       0.0   B
 fedora-release-identity-basic     noarch 42-0.3                     fedora     694.0   B
 fedora-repos                      noarch 42-0.2                     fedora       4.9 KiB
 fedora-repos-rawhide              noarch 42-0.2                     fedora       2.2 KiB
 file                              x86_64 5.45-7.fc41                fedora     103.5 KiB
 file-libs                         x86_64 5.45-7.fc41                fedora       9.9 MiB
 filesystem                        x86_64 3.18-29.fc42               fedora     106.0   B
 fonts-srpm-macros                 noarch 1:2.0.5-17.fc41            fedora      55.8 KiB
 forge-srpm-macros                 noarch 0.3.2-1.fc41               fedora      39.0 KiB
 fpc-srpm-macros                   noarch 1.3-13.fc41                fedora     144.0   B
 gdb-minimal                       x86_64 15.1-2.fc42                fedora      13.0 MiB
 gdbm                              x86_64 1:1.23-7.fc41              fedora     460.9 KiB
 gdbm-libs                         x86_64 1:1.23-7.fc41              fedora     121.9 KiB
 ghc-srpm-macros                   noarch 1.9.2-1.fc42               fedora     779.0   B
 glibc                             x86_64 2.40.9000-1.fc42           fedora       6.7 MiB
 glibc-common                      x86_64 2.40.9000-1.fc42           fedora       1.0 MiB
 glibc-gconv-extra                 x86_64 2.40.9000-1.fc42           fedora       8.1 MiB
 gmp                               x86_64 1:6.3.0-2.fc41             fedora     811.4 KiB
 gnat-srpm-macros                  noarch 6-6.fc41                   fedora       1.0 KiB
 go-srpm-macros                    noarch 3.6.0-3.fc41               fedora      60.8 KiB
 jansson                           x86_64 2.13.1-10.fc41             fedora      88.3 KiB
 kernel-srpm-macros                noarch 1.0-24.fc41                fedora       1.9 KiB
 keyutils-libs                     x86_64 1.6.3-4.fc41               fedora      54.4 KiB
 krb5-libs                         x86_64 1.21.3-2.fc41              fedora       2.3 MiB
 libacl                            x86_64 2.3.2-2.fc41               fedora      40.0 KiB
 libarchive                        x86_64 3.7.4-3.fc42               fedora     926.6 KiB
 libattr                           x86_64 2.5.2-4.fc41               fedora      28.5 KiB
 libblkid                          x86_64 2.40.2-8.fc42              fedora     262.5 KiB
 libbrotli                         x86_64 1.1.0-5.fc41               fedora     837.6 KiB
 libcap                            x86_64 2.70-4.fc41                fedora     220.2 KiB
 libcap-ng                         x86_64 0.8.5-3.fc41               fedora      69.2 KiB
 libcom_err                        x86_64 1.47.1-3.fc41              fedora      67.2 KiB
 libcurl                           x86_64 8.10.1-1.fc42              fedora     838.4 KiB
 libeconf                          x86_64 0.6.2-3.fc41               fedora      58.0 KiB
 libevent                          x86_64 2.1.12-14.fc41             fedora     895.7 KiB
 libfdisk                          x86_64 2.40.2-8.fc42              fedora     362.9 KiB
 libffi                            x86_64 3.4.6-3.fc42               fedora      86.4 KiB
 libgcc                            x86_64 14.2.1-3.fc42              fedora     274.6 KiB
 libgomp                           x86_64 14.2.1-3.fc42              fedora     523.8 KiB
 libidn2                           x86_64 2.3.7-2.fc41               fedora     329.1 KiB
 libmount                          x86_64 2.40.2-8.fc42              fedora     355.8 KiB
 libnghttp2                        x86_64 1.63.0-1.fc42              fedora     170.1 KiB
 libnsl2                           x86_64 2.0.1-2.fc41               fedora      57.9 KiB
 libpkgconf                        x86_64 2.3.0-1.fc42               fedora      78.2 KiB
 libpsl                            x86_64 0.21.5-4.fc41              fedora      80.5 KiB
 libpwquality                      x86_64 1.4.5-11.fc41              fedora     417.8 KiB
 libselinux                        x86_64 3.7-6.fc42                 fedora     181.1 KiB
 libsemanage                       x86_64 3.7-3.fc42                 fedora     298.0 KiB
 libsepol                          x86_64 3.7-3.fc42                 fedora     818.0 KiB
 libsmartcols                      x86_64 2.40.2-8.fc42              fedora     180.4 KiB
 libssh                            x86_64 0.11.1-1.fc42              fedora     569.6 KiB
 libssh-config                     noarch 0.11.1-1.fc42              fedora     277.0   B
 libstdc++                         x86_64 14.2.1-3.fc42              fedora       2.8 MiB
 libtasn1                          x86_64 4.19.0-9.fc41              fedora     175.7 KiB
 libtirpc                          x86_64 1.3.5-0.fc41               fedora     202.7 KiB
 libtool-ltdl                      x86_64 2.4.7-12.fc41              fedora      66.2 KiB
 libunistring                      x86_64 1.1-8.fc41                 fedora       1.7 MiB
 libuuid                           x86_64 2.40.2-8.fc42              fedora      41.4 KiB
 libverto                          x86_64 0.3.2-9.fc41               fedora      29.5 KiB
 libxcrypt                         x86_64 4.4.36-7.fc41              fedora     266.8 KiB
 libxml2                           x86_64 2.12.8-2.fc41              fedora       1.7 MiB
 libzstd                           x86_64 1.5.6-2.fc41               fedora     795.9 KiB
 lua-libs                          x86_64 5.4.6-6.fc41               fedora     285.0 KiB
 lua-srpm-macros                   noarch 1-14.fc41                  fedora       1.3 KiB
 lz4-libs                          x86_64 1.10.0-1.fc41              fedora     145.5 KiB
 mpfr                              x86_64 4.2.1-5.fc41               fedora     832.1 KiB
 ncurses-base                      noarch 6.5-2.20240629.fc41        fedora     326.3 KiB
 ncurses-libs                      x86_64 6.5-2.20240629.fc41        fedora     975.2 KiB
 ocaml-srpm-macros                 noarch 10-3.fc41                  fedora       1.9 KiB
 openblas-srpm-macros              noarch 2-18.fc41                  fedora     112.0   B
 openldap                          x86_64 2.6.8-5.fc41               fedora     644.2 KiB
 openssl-libs                      x86_64 1:3.2.2-8.fc42             fedora       7.8 MiB
 p11-kit                           x86_64 0.25.5-3.fc41              fedora       2.2 MiB
 p11-kit-trust                     x86_64 0.25.5-3.fc41              fedora     391.4 KiB
 package-notes-srpm-macros         noarch 0.5-12.fc41                fedora       1.6 KiB
 pam                               x86_64 1.6.1-6.fc42               fedora       1.8 MiB
 pam-libs                          x86_64 1.6.1-6.fc42               fedora     139.0 KiB
 pcre2                             x86_64 10.44-1.fc41.1             fedora     653.5 KiB
 pcre2-syntax                      noarch 10.44-1.fc41.1             fedora     251.6 KiB
 perl-srpm-macros                  noarch 1-56.fc41                  fedora     861.0   B
 pkgconf                           x86_64 2.3.0-1.fc42               fedora      88.6 KiB
 pkgconf-m4                        noarch 2.3.0-1.fc42               fedora      14.4 KiB
 pkgconf-pkg-config                x86_64 2.3.0-1.fc42               fedora     989.0   B
 popt                              x86_64 1.19-7.fc41                fedora     136.9 KiB
 publicsuffix-list-dafsa           noarch 20240107-4.fc41            fedora      67.5 KiB
 pyproject-srpm-macros             noarch 1.15.0-1.fc42              fedora       1.9 KiB
 python-srpm-macros                noarch 3.13-3.fc41                fedora      51.0 KiB
 qt5-srpm-macros                   noarch 5.15.15-1.fc42             fedora     500.0   B
 qt6-srpm-macros                   noarch 6.7.2-3.fc41               fedora     456.0   B
 readline                          x86_64 8.2-11.fc42                fedora     493.1 KiB
 rpm                               x86_64 4.19.94-1.fc42             fedora       3.1 MiB
 rpm-build-libs                    x86_64 4.19.94-1.fc42             fedora     206.7 KiB
 rpm-libs                          x86_64 4.19.94-1.fc42             fedora     722.1 KiB
 rpm-sequoia                       x86_64 1.7.0-2.fc41               fedora       2.4 MiB
 rust-srpm-macros                  noarch 26.3-3.fc42                fedora       4.8 KiB
 setup                             noarch 2.15.0-5.fc41              fedora     720.7 KiB
 sqlite-libs                       x86_64 3.46.0-4.fc41              fedora       1.4 MiB
 systemd-libs                      x86_64 256.5-1.fc42               fedora       2.0 MiB
 util-linux-core                   x86_64 2.40.2-8.fc42              fedora       1.5 MiB
 xxhash-libs                       x86_64 0.8.2-3.fc41               fedora      88.5 KiB
 xz-libs                           x86_64 1:5.6.2-2.fc41             fedora     214.4 KiB
 zig-srpm-macros                   noarch 1-3.fc41                   fedora       1.1 KiB
 zip                               x86_64 3.0-41.fc41                fedora     703.2 KiB
 zlib-ng-compat                    x86_64 2.2.2-1.fc42               copr_base  137.8 KiB
 zstd                              x86_64 1.5.6-2.fc41               fedora       1.7 MiB
Installing groups:
 Buildsystem building group                                                              

Transaction Summary:
 Installing:       153 packages

Total size of inbound packages is 53 MiB. Need to download 53 MiB.
After this operation, 180 MiB extra will be used (install 180 MiB, remove 0 B).
[  1/153] bzip2-0:1.0.8-19.fc41.x86_64  100% | 238.7 KiB/s |  52.5 KiB |  00m00s
[  2/153] bash-0:5.2.32-2.fc42.x86_64   100% |   3.6 MiB/s |   1.8 MiB |  00m01s
[  3/153] coreutils-0:9.5-9.fc42.x86_64 100% |   2.1 MiB/s |   1.1 MiB |  00m01s
[  4/153] diffutils-0:3.10-8.fc41.x86_6 100% |   7.5 MiB/s | 405.4 KiB |  00m00s
[  5/153] fedora-release-common-0:42-0. 100% | 535.1 KiB/s |  23.0 KiB |  00m00s
[  6/153] findutils-1:4.10.0-4.fc41.x86 100% |   9.4 MiB/s | 548.6 KiB |  00m00s
[  7/153] glibc-minimal-langpack-0:2.40 100% |   2.4 MiB/s | 120.9 KiB |  00m00s
[  8/153] cpio-0:2.15-2.fc41.x86_64     100% | 698.1 KiB/s | 291.8 KiB |  00m00s
[  9/153] grep-0:3.11-9.fc41.x86_64     100% |   5.9 MiB/s | 299.8 KiB |  00m00s
[ 10/153] gzip-0:1.13-2.fc41.x86_64     100% |   3.3 MiB/s | 170.2 KiB |  00m00s
[ 11/153] patch-0:2.7.6-25.fc41.x86_64  100% |   2.8 MiB/s | 131.0 KiB |  00m00s
[ 12/153] redhat-rpm-config-0:295-1.fc4 100% |   1.7 MiB/s |  82.4 KiB |  00m00s
[ 13/153] info-0:7.1.1-1.fc42.x86_64    100% |   1.8 MiB/s | 182.8 KiB |  00m00s
[ 14/153] rpm-build-0:4.19.94-1.fc42.x8 100% |   1.8 MiB/s |  83.1 KiB |  00m00s
[ 15/153] sed-0:4.9-3.fc41.x86_64       100% |   5.3 MiB/s | 317.7 KiB |  00m00s
[ 16/153] tar-2:1.35-4.fc41.x86_64      100% |  12.7 MiB/s | 860.7 KiB |  00m00s
[ 17/153] unzip-0:6.0-64.fc41.x86_64    100% |   3.5 MiB/s | 184.9 KiB |  00m00s
[ 18/153] which-0:2.21-42.fc41.x86_64   100% | 966.5 KiB/s |  41.6 KiB |  00m00s
[ 19/153] xz-1:5.6.2-2.fc41.x86_64      100% |   6.9 MiB/s | 471.5 KiB |  00m00s
[ 20/153] gawk-0:5.3.0-4.fc41.x86_64    100% |  14.9 MiB/s |   1.1 MiB |  00m00s
[ 21/153] util-linux-0:2.40.2-8.fc42.x8 100% |  11.3 MiB/s |   1.2 MiB |  00m00s
[ 22/153] filesystem-0:3.18-29.fc42.x86 100% |  15.8 MiB/s |   1.1 MiB |  00m00s
[ 23/153] ncurses-libs-0:6.5-2.20240629 100% |   6.4 MiB/s | 334.0 KiB |  00m00s
[ 24/153] glibc-0:2.40.9000-1.fc42.x86_ 100% |  13.3 MiB/s |   2.2 MiB |  00m00s
[ 25/153] shadow-utils-2:4.16.0-4.fc42. 100% |   2.8 MiB/s |   1.3 MiB |  00m00s
[ 26/153] coreutils-common-0:9.5-9.fc42 100% |  29.9 MiB/s |   2.1 MiB |  00m00s
[ 27/153] bzip2-libs-0:1.0.8-19.fc41.x8 100% | 218.7 KiB/s |  41.1 KiB |  00m00s
[ 28/153] libacl-0:2.3.2-2.fc41.x86_64  100% | 556.8 KiB/s |  24.5 KiB |  00m00s
[ 29/153] libattr-0:2.5.2-4.fc41.x86_64 100% | 422.6 KiB/s |  18.2 KiB |  00m00s
[ 30/153] gmp-1:6.3.0-2.fc41.x86_64     100% |   2.8 MiB/s | 318.0 KiB |  00m00s
[ 31/153] libcap-0:2.70-4.fc41.x86_64   100% |   1.9 MiB/s |  86.7 KiB |  00m00s
[ 32/153] libselinux-0:3.7-6.fc42.x86_6 100% |   2.0 MiB/s |  88.6 KiB |  00m00s
[ 33/153] systemd-libs-0:256.5-1.fc42.x 100% |   6.9 MiB/s | 730.4 KiB |  00m00s
[ 34/153] fedora-repos-0:42-0.2.noarch  100% |  59.1 KiB/s |   9.2 KiB |  00m00s
[ 35/153] glibc-common-0:2.40.9000-1.fc 100% |   4.0 MiB/s | 409.4 KiB |  00m00s
[ 36/153] pcre2-0:10.44-1.fc41.1.x86_64 100% |   1.7 MiB/s | 243.1 KiB |  00m00s
[ 37/153] ed-0:1.20.2-2.fc41.x86_64     100% | 588.6 KiB/s |  81.8 KiB |  00m00s
[ 38/153] ansible-srpm-macros-0:1-16.fc 100% | 442.0 KiB/s |  20.8 KiB |  00m00s
[ 39/153] build-reproducibility-srpm-ma 100% | 246.6 KiB/s |  10.6 KiB |  00m00s
[ 40/153] dwz-0:0.15-7.fc41.x86_64      100% |   1.8 MiB/s | 138.0 KiB |  00m00s
[ 41/153] efi-srpm-macros-0:5-12.fc41.n 100% | 520.4 KiB/s |  22.4 KiB |  00m00s
[ 42/153] fonts-srpm-macros-1:2.0.5-17. 100% | 627.1 KiB/s |  27.0 KiB |  00m00s
[ 43/153] file-0:5.45-7.fc41.x86_64     100% | 927.0 KiB/s |  49.1 KiB |  00m00s
[ 44/153] forge-srpm-macros-0:0.3.2-1.f 100% | 458.2 KiB/s |  19.7 KiB |  00m00s
[ 45/153] fpc-srpm-macros-0:1.3-13.fc41 100% | 185.2 KiB/s |   8.0 KiB |  00m00s
[ 46/153] openssl-libs-1:3.2.2-8.fc42.x 100% |   4.2 MiB/s |   2.3 MiB |  00m01s
[ 47/153] ghc-srpm-macros-0:1.9.2-1.fc4 100% | 212.0 KiB/s |   9.1 KiB |  00m00s
[ 48/153] gnat-srpm-macros-0:6-6.fc41.n 100% | 203.5 KiB/s |   9.0 KiB |  00m00s
[ 49/153] go-srpm-macros-0:3.6.0-3.fc41 100% | 594.7 KiB/s |  28.0 KiB |  00m00s
[ 50/153] kernel-srpm-macros-0:1.0-24.f 100% | 229.5 KiB/s |   9.9 KiB |  00m00s
[ 51/153] lua-srpm-macros-0:1-14.fc41.n 100% | 201.8 KiB/s |   8.9 KiB |  00m00s
[ 52/153] ocaml-srpm-macros-0:10-3.fc41 100% | 209.1 KiB/s |   9.2 KiB |  00m00s
[ 53/153] openblas-srpm-macros-0:2-18.f 100% | 179.4 KiB/s |   7.7 KiB |  00m00s
[ 54/153] package-notes-srpm-macros-0:0 100% | 218.4 KiB/s |   9.8 KiB |  00m00s
[ 55/153] perl-srpm-macros-0:1-56.fc41. 100% | 193.5 KiB/s |   8.5 KiB |  00m00s
[ 56/153] pyproject-srpm-macros-0:1.15. 100% | 315.1 KiB/s |  13.5 KiB |  00m00s
[ 57/153] python-srpm-macros-0:3.13-3.f 100% | 504.7 KiB/s |  23.7 KiB |  00m00s
[ 58/153] qt5-srpm-macros-0:5.15.15-1.f 100% | 202.2 KiB/s |   8.9 KiB |  00m00s
[ 59/153] qt6-srpm-macros-0:6.7.2-3.fc4 100% | 212.3 KiB/s |   9.1 KiB |  00m00s
[ 60/153] rust-srpm-macros-0:26.3-3.fc4 100% | 275.0 KiB/s |  12.1 KiB |  00m00s
[ 61/153] zig-srpm-macros-0:1-3.fc41.no 100% | 188.9 KiB/s |   8.1 KiB |  00m00s
[ 62/153] debugedit-0:5.0-17.fc41.x86_6 100% |   1.7 MiB/s |  80.1 KiB |  00m00s
[ 63/153] zip-0:3.0-41.fc41.x86_64      100% |   3.0 MiB/s | 264.8 KiB |  00m00s
[ 64/153] rpm-0:4.19.94-1.fc42.x86_64   100% |   3.5 MiB/s | 547.8 KiB |  00m00s
[ 65/153] elfutils-0:0.191-8.fc41.x86_6 100% |   8.8 MiB/s | 529.4 KiB |  00m00s
[ 66/153] elfutils-libelf-0:0.191-8.fc4 100% |   2.7 MiB/s | 207.6 KiB |  00m00s
[ 67/153] popt-0:1.19-7.fc41.x86_64     100% |   1.5 MiB/s |  65.9 KiB |  00m00s
[ 68/153] libarchive-0:3.7.4-3.fc42.x86 100% |   3.6 MiB/s | 409.2 KiB |  00m00s
[ 69/153] rpm-build-libs-0:4.19.94-1.fc 100% |   2.2 MiB/s |  99.1 KiB |  00m00s
[ 70/153] readline-0:8.2-11.fc42.x86_64 100% |   2.7 MiB/s | 213.4 KiB |  00m00s
[ 71/153] zstd-0:1.5.6-2.fc41.x86_64    100% |   8.1 MiB/s | 481.5 KiB |  00m00s
[ 72/153] rpm-libs-0:4.19.94-1.fc42.x86 100% |   3.3 MiB/s | 309.6 KiB |  00m00s
[ 73/153] audit-libs-0:4.0.2-1.fc41.x86 100% |   2.0 MiB/s | 126.2 KiB |  00m00s
[ 74/153] libeconf-0:0.6.2-3.fc41.x86_6 100% | 748.3 KiB/s |  32.2 KiB |  00m00s
[ 75/153] libsemanage-0:3.7-3.fc42.x86_ 100% |   1.9 MiB/s | 117.2 KiB |  00m00s
[ 76/153] pam-libs-0:1.6.1-6.fc42.x86_6 100% |   1.3 MiB/s |  57.2 KiB |  00m00s
[ 77/153] libxcrypt-0:4.4.36-7.fc41.x86 100% |   1.9 MiB/s | 118.5 KiB |  00m00s
[ 78/153] xz-libs-1:5.6.2-2.fc41.x86_64 100% |   2.4 MiB/s | 111.8 KiB |  00m00s
[ 79/153] setup-0:2.15.0-5.fc41.noarch  100% |   2.3 MiB/s | 154.4 KiB |  00m00s
[ 80/153] libblkid-0:2.40.2-8.fc42.x86_ 100% |   2.7 MiB/s | 125.0 KiB |  00m00s
[ 81/153] mpfr-0:4.2.1-5.fc41.x86_64    100% |   3.5 MiB/s | 346.3 KiB |  00m00s
[ 82/153] libcap-ng-0:0.8.5-3.fc41.x86_ 100% | 692.8 KiB/s |  32.6 KiB |  00m00s
[ 83/153] libfdisk-0:2.40.2-8.fc42.x86_ 100% |   3.3 MiB/s | 159.6 KiB |  00m00s
[ 84/153] libsmartcols-0:2.40.2-8.fc42. 100% |   1.5 MiB/s |  83.9 KiB |  00m00s
[ 85/153] libmount-0:2.40.2-8.fc42.x86_ 100% |   2.3 MiB/s | 156.1 KiB |  00m00s
[ 86/153] libuuid-0:2.40.2-8.fc42.x86_6 100% | 673.9 KiB/s |  29.0 KiB |  00m00s
[ 87/153] basesystem-0:11-21.fc41.noarc 100% | 171.4 KiB/s |   7.4 KiB |  00m00s
[ 88/153] util-linux-core-0:2.40.2-8.fc 100% |   4.4 MiB/s | 537.3 KiB |  00m00s
[ 89/153] libgcc-0:14.2.1-3.fc42.x86_64 100% |   1.5 MiB/s | 133.3 KiB |  00m00s
[ 90/153] ncurses-base-0:6.5-2.20240629 100% |   1.6 MiB/s |  88.4 KiB |  00m00s
[ 91/153] glibc-gconv-extra-0:2.40.9000 100% |   7.0 MiB/s |   1.7 MiB |  00m00s
[ 92/153] crypto-policies-0:20240828-1. 100% |   1.8 MiB/s |  94.6 KiB |  00m00s
[ 93/153] ca-certificates-0:2024.2.69_v 100% |   6.1 MiB/s | 944.3 KiB |  00m00s
[ 94/153] libsepol-0:3.7-3.fc42.x86_64  100% |   1.7 MiB/s | 342.2 KiB |  00m00s
[ 95/153] fedora-gpg-keys-0:42-0.2.noar 100% |   2.4 MiB/s | 133.6 KiB |  00m00s
[ 96/153] fedora-repos-rawhide-0:42-0.2 100% | 203.3 KiB/s |   8.7 KiB |  00m00s
[ 97/153] pcre2-syntax-0:10.44-1.fc41.1 100% |   1.3 MiB/s | 149.9 KiB |  00m00s
[ 98/153] add-determinism-0:0.3.6-1.fc4 100% |   7.3 MiB/s | 851.8 KiB |  00m00s
[ 99/153] file-libs-0:5.45-7.fc41.x86_6 100% |   6.4 MiB/s | 762.0 KiB |  00m00s
[100/153] elfutils-debuginfod-client-0: 100% | 809.5 KiB/s |  37.2 KiB |  00m00s
[101/153] elfutils-libs-0:0.191-8.fc41. 100% |   4.0 MiB/s | 257.5 KiB |  00m00s
[102/153] curl-0:8.10.1-1.fc42.x86_64   100% |   1.8 MiB/s | 221.1 KiB |  00m00s
[103/153] libzstd-0:1.5.6-2.fc41.x86_64 100% |   4.5 MiB/s | 310.3 KiB |  00m00s
[104/153] libstdc++-0:14.2.1-3.fc42.x86 100% |   7.5 MiB/s | 888.0 KiB |  00m00s
[105/153] lz4-libs-0:1.10.0-1.fc41.x86_ 100% |   1.4 MiB/s |  70.7 KiB |  00m00s
[106/153] lua-libs-0:5.4.6-6.fc41.x86_6 100% |   2.4 MiB/s | 132.0 KiB |  00m00s
[107/153] libgomp-0:14.2.1-3.fc42.x86_6 100% |   5.0 MiB/s | 355.2 KiB |  00m00s
[108/153] libxml2-0:2.12.8-2.fc41.x86_6 100% |   3.2 MiB/s | 687.3 KiB |  00m00s
[109/153] sqlite-libs-0:3.46.0-4.fc41.x 100% |   7.2 MiB/s | 712.4 KiB |  00m00s
[110/153] rpm-sequoia-0:1.7.0-2.fc41.x8 100% |   7.9 MiB/s | 892.5 KiB |  00m00s
[111/153] elfutils-default-yama-scope-0 100% | 256.3 KiB/s |  12.3 KiB |  00m00s
[112/153] zlib-ng-compat-0:2.2.2-1.fc42 100% |   1.6 MiB/s |  77.3 KiB |  00m00s
[113/153] authselect-0:1.5.0-7.fc41.x86 100% |   2.7 MiB/s | 145.7 KiB |  00m00s
[114/153] pam-0:1.6.1-6.fc42.x86_64     100% |   6.0 MiB/s | 554.2 KiB |  00m00s
[115/153] gdbm-libs-1:1.23-7.fc41.x86_6 100% |   1.0 MiB/s |  56.3 KiB |  00m00s
[116/153] libnsl2-0:2.0.1-2.fc41.x86_64 100% | 658.0 KiB/s |  29.6 KiB |  00m00s
[117/153] libpwquality-0:1.4.5-11.fc41. 100% |   2.3 MiB/s | 119.1 KiB |  00m00s
[118/153] libtirpc-0:1.3.5-0.fc41.x86_6 100% |   1.5 MiB/s |  94.2 KiB |  00m00s
[119/153] authselect-libs-0:1.5.0-7.fc4 100% |   3.6 MiB/s | 218.1 KiB |  00m00s
[120/153] cracklib-0:2.9.11-6.fc41.x86_ 100% |   1.8 MiB/s |  92.0 KiB |  00m00s
[121/153] libcom_err-0:1.47.1-3.fc41.x8 100% | 600.3 KiB/s |  26.4 KiB |  00m00s
[122/153] keyutils-libs-0:1.6.3-4.fc41. 100% | 719.3 KiB/s |  31.6 KiB |  00m00s
[123/153] libverto-0:0.3.2-9.fc41.x86_6 100% | 470.3 KiB/s |  20.7 KiB |  00m00s
[124/153] alternatives-0:1.30-1.fc41.x8 100% | 772.1 KiB/s |  42.5 KiB |  00m00s
[125/153] binutils-0:2.43.50-1.fc42.x86 100% |  60.2 MiB/s |   6.4 MiB |  00m00s
[126/153] krb5-libs-0:1.21.3-2.fc41.x86 100% |   4.0 MiB/s | 757.4 KiB |  00m00s
[127/153] jansson-0:2.13.1-10.fc41.x86_ 100% | 987.3 KiB/s |  44.4 KiB |  00m00s
[128/153] pkgconf-pkg-config-0:2.3.0-1. 100% | 227.5 KiB/s |  10.0 KiB |  00m00s
[129/153] pkgconf-0:2.3.0-1.fc42.x86_64 100% | 922.0 KiB/s |  45.2 KiB |  00m00s
[130/153] pkgconf-m4-0:2.3.0-1.fc42.noa 100% | 333.1 KiB/s |  14.3 KiB |  00m00s
[131/153] libpkgconf-0:2.3.0-1.fc42.x86 100% | 855.3 KiB/s |  38.5 KiB |  00m00s
[132/153] libffi-0:3.4.6-3.fc42.x86_64  100% | 908.9 KiB/s |  40.0 KiB |  00m00s
[133/153] gdbm-1:1.23-7.fc41.x86_64     100% |   2.2 MiB/s | 151.8 KiB |  00m00s
[134/153] libtasn1-0:4.19.0-9.fc41.x86_ 100% |   1.5 MiB/s |  74.2 KiB |  00m00s
[135/153] p11-kit-0:0.25.5-3.fc41.x86_6 100% |   6.1 MiB/s | 490.9 KiB |  00m00s
[136/153] p11-kit-trust-0:0.25.5-3.fc41 100% |   2.0 MiB/s | 132.1 KiB |  00m00s
[137/153] fedora-release-0:42-0.3.noarc 100% | 284.4 KiB/s |  12.2 KiB |  00m00s
[138/153] xxhash-libs-0:0.8.2-3.fc41.x8 100% | 757.5 KiB/s |  37.1 KiB |  00m00s
[139/153] fedora-release-identity-basic 100% | 302.7 KiB/s |  13.0 KiB |  00m00s
[140/153] libbrotli-0:1.1.0-5.fc41.x86_ 100% |   4.9 MiB/s | 340.5 KiB |  00m00s
[141/153] libcurl-0:8.10.1-1.fc42.x86_6 100% |   3.6 MiB/s | 371.2 KiB |  00m00s
[142/153] libidn2-0:2.3.7-2.fc41.x86_64 100% |   2.3 MiB/s | 118.4 KiB |  00m00s
[143/153] libnghttp2-0:1.63.0-1.fc42.x8 100% |   1.4 MiB/s |  76.7 KiB |  00m00s
[144/153] libpsl-0:0.21.5-4.fc41.x86_64 100% |   1.4 MiB/s |  64.1 KiB |  00m00s
[145/153] gdb-minimal-0:15.1-2.fc42.x86 100% |  15.9 MiB/s |   4.3 MiB |  00m00s
[146/153] libssh-0:0.11.1-1.fc42.x86_64 100% |   2.9 MiB/s | 231.9 KiB |  00m00s
[147/153] openldap-0:2.6.8-5.fc41.x86_6 100% |   4.1 MiB/s | 255.6 KiB |  00m00s
[148/153] libunistring-0:1.1-8.fc41.x86 100% |   8.3 MiB/s | 544.8 KiB |  00m00s
[149/153] publicsuffix-list-dafsa-0:202 100% |   1.1 MiB/s |  58.3 KiB |  00m00s
[150/153] libssh-config-0:0.11.1-1.fc42 100% | 218.3 KiB/s |   9.4 KiB |  00m00s
[151/153] libtool-ltdl-0:2.4.7-12.fc41. 100% | 808.9 KiB/s |  35.6 KiB |  00m00s
[152/153] cyrus-sasl-lib-0:2.1.28-27.fc 100% |  10.3 MiB/s | 794.9 KiB |  00m00s
[153/153] libevent-0:2.1.12-14.fc41.x86 100% |   3.0 MiB/s | 257.5 KiB |  00m00s
--------------------------------------------------------------------------------
[153/153] Total                         100% |  12.0 MiB/s |  53.2 MiB |  00m04s
Running transaction
Importing PGP key 0x105EF944:
 UserID     : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
 Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing PGP key 0x105EF944:
 UserID     : "Fedora (42) <fedora-42-primary@fedoraproject.org>"
 Fingerprint: B0F4950458F69E1150C6C5EDC8AC4916105EF944
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-42-primary
The key was successfully imported.
Importing PGP key 0xE99D6AD1:
 UserID     : "Fedora (41) <fedora-41-primary@fedoraproject.org>"
 Fingerprint: 466CF2D8B60BC3057AA9453ED0622462E99D6AD1
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-41-primary
The key was successfully imported.
Importing PGP key 0x31645531:
 UserID     : "Fedora (43) <fedora-43-primary@fedoraproject.org>"
 Fingerprint: C6E7F081CF80E13146676E88829B606631645531
 From       : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary
The key was successfully imported.
[  1/155] Verify package files          100% | 674.0   B/s | 153.0   B |  00m00s
[  2/155] Prepare transaction           100% |   1.4 KiB/s | 153.0   B |  00m00s
[  3/155] Installing libgcc-0:14.2.1-3. 100% |  89.9 MiB/s | 276.3 KiB |  00m00s
[  4/155] Installing libssh-config-0:0. 100% |   0.0   B/s | 816.0   B |  00m00s
[  5/155] Installing publicsuffix-list- 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[  6/155] Installing fedora-release-ide 100% |   0.0   B/s | 952.0   B |  00m00s
[  7/155] Installing fedora-repos-rawhi 100% |   2.4 MiB/s |   2.4 KiB |  00m00s
[  8/155] Installing fedora-gpg-keys-0: 100% |  15.3 MiB/s | 172.2 KiB |  00m00s
[  9/155] Installing fedora-repos-0:42- 100% |   5.6 MiB/s |   5.7 KiB |  00m00s
[ 10/155] Installing fedora-release-com 100% |  11.6 MiB/s |  23.7 KiB |  00m00s
[ 11/155] Installing fedora-release-0:4 100% |   0.0   B/s | 124.0   B |  00m00s
[ 12/155] Installing setup-0:2.15.0-5.f 100% |  33.8 MiB/s | 726.1 KiB |  00m00s
[ 13/155] Installing filesystem-0:3.18- 100% |   1.2 MiB/s | 212.6 KiB |  00m00s
[ 14/155] Installing basesystem-0:11-21 100% |   0.0   B/s | 124.0   B |  00m00s
[ 15/155] Installing pkgconf-m4-0:2.3.0 100% |  14.5 MiB/s |  14.8 KiB |  00m00s
[ 16/155] Installing pcre2-syntax-0:10. 100% |  82.7 MiB/s | 254.1 KiB |  00m00s
[ 17/155] Installing ncurses-base-0:6.5 100% |  31.2 MiB/s | 351.7 KiB |  00m00s
[ 18/155] Installing glibc-minimal-lang 100% | 121.1 KiB/s | 124.0   B |  00m00s
[ 19/155] Installing ncurses-libs-0:6.5 100% | 106.5 MiB/s | 981.8 KiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[ 20/155] Installing glibc-0:2.40.9000- 100% | 106.4 MiB/s |   6.7 MiB |  00m00s
[ 21/155] Installing bash-0:5.2.32-2.fc 100% | 199.2 MiB/s |   8.2 MiB |  00m00s
[ 22/155] Installing glibc-common-0:2.4 100% |  95.2 MiB/s |   1.0 MiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[ 23/155] Installing glibc-gconv-extra- 100% |  99.0 MiB/s |   8.2 MiB |  00m00s
[ 24/155] Installing zlib-ng-compat-0:2 100% |  67.7 MiB/s | 138.7 KiB |  00m00s
[ 25/155] Installing bzip2-libs-0:1.0.8 100% |  39.9 MiB/s |  81.8 KiB |  00m00s
[ 26/155] Installing xz-libs-1:5.6.2-2. 100% |  70.1 MiB/s | 215.5 KiB |  00m00s
[ 27/155] Installing popt-0:1.19-7.fc41 100% |  23.4 MiB/s | 143.5 KiB |  00m00s
[ 28/155] Installing readline-0:8.2-11. 100% | 120.9 MiB/s | 495.3 KiB |  00m00s
[ 29/155] Installing libuuid-0:2.40.2-8 100% |  41.5 MiB/s |  42.5 KiB |  00m00s
[ 30/155] Installing libblkid-0:2.40.2- 100% | 128.7 MiB/s | 263.6 KiB |  00m00s
[ 31/155] Installing gmp-1:6.3.0-2.fc41 100% | 158.9 MiB/s | 813.7 KiB |  00m00s
[ 32/155] Installing libattr-0:2.5.2-4. 100% |  28.8 MiB/s |  29.5 KiB |  00m00s
[ 33/155] Installing libacl-0:2.3.2-2.f 100% |  39.8 MiB/s |  40.7 KiB |  00m00s
[ 34/155] Installing libxcrypt-0:4.4.36 100% |  87.7 MiB/s | 269.5 KiB |  00m00s
[ 35/155] Installing libstdc++-0:14.2.1 100% | 185.0 MiB/s |   2.8 MiB |  00m00s
[ 36/155] Installing libzstd-0:1.5.6-2. 100% | 194.6 MiB/s | 797.2 KiB |  00m00s
[ 37/155] Installing elfutils-libelf-0: 100% | 194.9 MiB/s |   1.2 MiB |  00m00s
[ 38/155] Installing libeconf-0:0.6.2-3 100% |  29.1 MiB/s |  59.7 KiB |  00m00s
[ 39/155] Installing gdbm-libs-1:1.23-7 100% |  60.3 MiB/s | 123.6 KiB |  00m00s
[ 40/155] Installing dwz-0:0.15-7.fc41. 100% |  95.2 MiB/s | 292.3 KiB |  00m00s
[ 41/155] Installing mpfr-0:4.2.1-5.fc4 100% | 135.7 MiB/s | 833.7 KiB |  00m00s
[ 42/155] Installing gawk-0:5.3.0-4.fc4 100% | 133.2 MiB/s |   1.7 MiB |  00m00s
[ 43/155] Installing unzip-0:6.0-64.fc4 100% | 127.0 MiB/s | 390.3 KiB |  00m00s
[ 44/155] Installing file-libs-0:5.45-7 100% | 382.1 MiB/s |   9.9 MiB |  00m00s
[ 45/155] Installing file-0:5.45-7.fc41 100% |   6.0 MiB/s | 105.0 KiB |  00m00s
[ 46/155] Installing crypto-policies-0: 100% |  11.4 MiB/s | 163.2 KiB |  00m00s
[ 47/155] Installing pcre2-0:10.44-1.fc 100% | 159.9 MiB/s | 654.9 KiB |  00m00s
[ 48/155] Installing grep-0:3.11-9.fc41 100% |  91.2 MiB/s |   1.0 MiB |  00m00s
[ 49/155] Installing xz-1:5.6.2-2.fc41. 100% |  92.7 MiB/s |   1.2 MiB |  00m00s
[ 50/155] Installing libcap-ng-0:0.8.5- 100% |  34.7 MiB/s |  71.0 KiB |  00m00s
[ 51/155] Installing audit-libs-0:4.0.2 100% | 108.5 MiB/s | 333.4 KiB |  00m00s
[ 52/155] Installing pam-libs-0:1.6.1-6 100% |  69.0 MiB/s | 141.3 KiB |  00m00s
[ 53/155] Installing libcap-0:2.70-4.fc 100% |  55.0 MiB/s | 225.2 KiB |  00m00s
[ 54/155] Installing systemd-libs-0:256 100% | 135.6 MiB/s |   2.0 MiB |  00m00s
[ 55/155] Installing libsmartcols-0:2.4 100% |  88.6 MiB/s | 181.4 KiB |  00m00s
[ 56/155] Installing libsepol-0:3.7-3.f 100% | 160.0 MiB/s | 819.0 KiB |  00m00s
[ 57/155] Installing libselinux-0:3.7-6 100% |  89.0 MiB/s | 182.3 KiB |  00m00s
[ 58/155] Installing sed-0:4.9-3.fc41.x 100% |  84.9 MiB/s | 869.7 KiB |  00m00s
[ 59/155] Installing findutils-1:4.10.0 100% | 142.9 MiB/s |   1.9 MiB |  00m00s
[ 60/155] Installing libmount-0:2.40.2- 100% | 116.2 MiB/s | 356.9 KiB |  00m00s
[ 61/155] Installing lz4-libs-0:1.10.0- 100% |  71.6 MiB/s | 146.6 KiB |  00m00s
[ 62/155] Installing lua-libs-0:5.4.6-6 100% | 139.8 MiB/s | 286.2 KiB |  00m00s
[ 63/155] Installing libcom_err-0:1.47. 100% |  66.7 MiB/s |  68.3 KiB |  00m00s
[ 64/155] Installing alternatives-0:1.3 100% |  66.3 MiB/s |  67.9 KiB |  00m00s
[ 65/155] Installing libffi-0:3.4.6-3.f 100% |  42.9 MiB/s |  87.8 KiB |  00m00s
[ 66/155] Installing libtasn1-0:4.19.0- 100% |  86.7 MiB/s | 177.5 KiB |  00m00s
[ 67/155] Installing p11-kit-0:0.25.5-3 100% | 116.2 MiB/s |   2.2 MiB |  00m00s
[ 68/155] Installing libunistring-0:1.1 100% | 192.3 MiB/s |   1.7 MiB |  00m00s
[ 69/155] Installing libidn2-0:2.3.7-2. 100% |  54.5 MiB/s | 335.1 KiB |  00m00s
[ 70/155] Installing libpsl-0:0.21.5-4. 100% |  79.7 MiB/s |  81.7 KiB |  00m00s
[ 71/155] Installing p11-kit-trust-0:0. 100% |  21.3 MiB/s | 393.1 KiB |  00m00s
[ 72/155] Installing zstd-0:1.5.6-2.fc4 100% | 187.9 MiB/s |   1.7 MiB |  00m00s
[ 73/155] Installing util-linux-core-0: 100% | 109.1 MiB/s |   1.5 MiB |  00m00s
[ 74/155] Installing tar-2:1.35-4.fc41. 100% | 174.0 MiB/s |   3.0 MiB |  00m00s
[ 75/155] Installing libsemanage-0:3.7- 100% |  73.2 MiB/s | 299.8 KiB |  00m00s
[ 76/155] Installing shadow-utils-2:4.1 100% | 106.3 MiB/s |   4.1 MiB |  00m00s
[ 77/155] Installing zip-0:3.0-41.fc41. 100% | 138.1 MiB/s | 707.1 KiB |  00m00s
[ 78/155] Installing gdbm-1:1.23-7.fc41 100% |  91.0 MiB/s | 465.8 KiB |  00m00s
[ 79/155] Installing cyrus-sasl-lib-0:2 100% | 230.6 MiB/s |   2.3 MiB |  00m00s
[ 80/155] Installing libfdisk-0:2.40.2- 100% | 177.7 MiB/s | 364.0 KiB |  00m00s
[ 81/155] Installing libxml2-0:2.12.8-2 100% | 214.0 MiB/s |   1.7 MiB |  00m00s
[ 82/155] Installing bzip2-0:1.0.8-19.f 100% |  48.9 MiB/s | 100.2 KiB |  00m00s
[ 83/155] Installing add-determinism-0: 100% | 187.2 MiB/s |   2.2 MiB |  00m00s
[ 84/155] Installing build-reproducibil 100% |   0.0   B/s |   1.0 KiB |  00m00s
[ 85/155] Installing sqlite-libs-0:3.46 100% | 204.2 MiB/s |   1.4 MiB |  00m00s
[ 86/155] Installing ed-0:1.20.2-2.fc41 100% |  72.8 MiB/s | 149.2 KiB |  00m00s
[ 87/155] Installing patch-0:2.7.6-25.f 100% | 131.0 MiB/s | 268.2 KiB |  00m00s
[ 88/155] Installing elfutils-default-y 100% | 145.9 KiB/s |   2.0 KiB |  00m00s
[ 89/155] Installing elfutils-libs-0:0. 100% | 105.5 MiB/s | 648.0 KiB |  00m00s
[ 90/155] Installing cpio-0:2.15-2.fc41 100% | 110.0 MiB/s |   1.1 MiB |  00m00s
[ 91/155] Installing diffutils-0:3.10-8 100% | 122.3 MiB/s |   1.6 MiB |  00m00s
[ 92/155] Installing libgomp-0:14.2.1-3 100% | 128.2 MiB/s | 525.2 KiB |  00m00s
[ 93/155] Installing keyutils-libs-0:1. 100% |  54.5 MiB/s |  55.8 KiB |  00m00s
[ 94/155] Installing libverto-0:0.3.2-9 100% |  15.3 MiB/s |  31.3 KiB |  00m00s
[ 95/155] Installing jansson-0:2.13.1-1 100% |  43.8 MiB/s |  89.7 KiB |  00m00s
[ 96/155] Installing libpkgconf-0:2.3.0 100% |  77.5 MiB/s |  79.3 KiB |  00m00s
[ 97/155] Installing pkgconf-0:2.3.0-1. 100% |  44.5 MiB/s |  91.1 KiB |  00m00s
[ 98/155] Installing pkgconf-pkg-config 100% |   1.7 MiB/s |   1.8 KiB |  00m00s
[ 99/155] Installing xxhash-libs-0:0.8. 100% |  43.9 MiB/s |  89.9 KiB |  00m00s
[100/155] Installing libbrotli-0:1.1.0- 100% | 164.0 MiB/s | 839.9 KiB |  00m00s
[101/155] Installing libnghttp2-0:1.63. 100% |  83.6 MiB/s | 171.2 KiB |  00m00s
[102/155] Installing libtool-ltdl-0:2.4 100% |  32.9 MiB/s |  67.3 KiB |  00m00s
[103/155] Installing rust-srpm-macros-0 100% |   5.4 MiB/s |   5.6 KiB |  00m00s
[104/155] Installing qt6-srpm-macros-0: 100% | 714.8 KiB/s | 732.0   B |  00m00s
[105/155] Installing qt5-srpm-macros-0: 100% | 757.8 KiB/s | 776.0   B |  00m00s
[106/155] Installing perl-srpm-macros-0 100% |   0.0   B/s |   1.1 KiB |  00m00s
[107/155] Installing package-notes-srpm 100% |   2.0 MiB/s |   2.0 KiB |  00m00s
[108/155] Installing openblas-srpm-macr 100% |   0.0   B/s | 392.0   B |  00m00s
[109/155] Installing ocaml-srpm-macros- 100% |   2.1 MiB/s |   2.2 KiB |  00m00s
[110/155] Installing kernel-srpm-macros 100% |   2.3 MiB/s |   2.3 KiB |  00m00s
[111/155] Installing gnat-srpm-macros-0 100% |   0.0   B/s |   1.3 KiB |  00m00s
[112/155] Installing ghc-srpm-macros-0: 100% |   0.0   B/s |   1.0 KiB |  00m00s
[113/155] Installing fpc-srpm-macros-0: 100% |   0.0   B/s | 420.0   B |  00m00s
[114/155] Installing ansible-srpm-macro 100% |  17.7 MiB/s |  36.2 KiB |  00m00s
[115/155] Installing coreutils-common-0 100% | 183.4 MiB/s |  11.2 MiB |  00m00s
[116/155] Installing openssl-libs-1:3.2 100% | 211.6 MiB/s |   7.8 MiB |  00m00s
[117/155] Installing coreutils-0:9.5-9. 100% | 116.7 MiB/s |   5.7 MiB |  00m00s
[118/155] Installing ca-certificates-0: 100% |   1.1 MiB/s |   2.4 MiB |  00m02s
[119/155] Installing krb5-libs-0:1.21.3 100% | 127.7 MiB/s |   2.3 MiB |  00m00s
[120/155] Installing libarchive-0:3.7.4 100% | 129.5 MiB/s | 928.6 KiB |  00m00s
[121/155] Installing libtirpc-0:1.3.5-0 100% |  66.6 MiB/s | 204.5 KiB |  00m00s
[122/155] Installing gzip-0:1.13-2.fc41 100% |  64.2 MiB/s | 394.6 KiB |  00m00s
[123/155] Installing authselect-libs-0: 100% |  62.6 MiB/s | 833.2 KiB |  00m00s
[124/155] Installing cracklib-0:2.9.11- 100% |  22.2 MiB/s | 250.3 KiB |  00m00s
[125/155] Installing libpwquality-0:1.4 100% |  35.0 MiB/s | 430.1 KiB |  00m00s
[126/155] Installing libnsl2-0:2.0.1-2. 100% |  19.2 MiB/s |  59.1 KiB |  00m00s
[127/155] Installing pam-0:1.6.1-6.fc42 100% |  56.9 MiB/s |   1.9 MiB |  00m00s
[128/155] Installing libssh-0:0.11.1-1. 100% | 111.7 MiB/s | 571.7 KiB |  00m00s
[129/155] Installing rpm-sequoia-0:1.7. 100% | 197.3 MiB/s |   2.4 MiB |  00m00s
[130/155] Installing rpm-libs-0:4.19.94 100% | 141.3 MiB/s | 723.6 KiB |  00m00s
[131/155] Installing rpm-build-libs-0:4 100% | 101.3 MiB/s | 207.5 KiB |  00m00s
[132/155] Installing libevent-0:2.1.12- 100% | 146.4 MiB/s | 899.5 KiB |  00m00s
[133/155] Installing openldap-0:2.6.8-5 100% | 105.5 MiB/s | 648.0 KiB |  00m00s
[134/155] Installing libcurl-0:8.10.1-1 100% | 164.0 MiB/s | 839.5 KiB |  00m00s
[135/155] Installing elfutils-debuginfo 100% |  21.8 MiB/s |  66.9 KiB |  00m00s
[136/155] Installing elfutils-0:0.191-8 100% | 170.7 MiB/s |   2.6 MiB |  00m00s
[137/155] Installing binutils-0:2.43.50 100% | 255.2 MiB/s |  27.6 MiB |  00m00s
[138/155] Installing gdb-minimal-0:15.1 100% | 288.8 MiB/s |  13.0 MiB |  00m00s
[139/155] Installing debugedit-0:5.0-17 100% |  98.6 MiB/s | 202.0 KiB |  00m00s
[140/155] Installing curl-0:8.10.1-1.fc 100% |  24.7 MiB/s | 455.7 KiB |  00m00s
[141/155] Installing rpm-0:4.19.94-1.fc 100% |  89.5 MiB/s |   2.5 MiB |  00m00s
[142/155] Installing efi-srpm-macros-0: 100% |  40.2 MiB/s |  41.2 KiB |  00m00s
[143/155] Installing lua-srpm-macros-0: 100% |   1.9 MiB/s |   1.9 KiB |  00m00s
[144/155] Installing zig-srpm-macros-0: 100% |   0.0   B/s |   1.7 KiB |  00m00s
[145/155] Installing fonts-srpm-macros- 100% |  55.7 MiB/s |  57.0 KiB |  00m00s
[146/155] Installing forge-srpm-macros- 100% |  39.4 MiB/s |  40.4 KiB |  00m00s
[147/155] Installing go-srpm-macros-0:3 100% |  60.5 MiB/s |  62.0 KiB |  00m00s
[148/155] Installing python-srpm-macros 100% |  50.9 MiB/s |  52.2 KiB |  00m00s
[149/155] Installing redhat-rpm-config- 100% |  62.9 MiB/s | 193.2 KiB |  00m00s
[150/155] Installing rpm-build-0:4.19.9 100% |  49.5 MiB/s | 202.9 KiB |  00m00s
[151/155] Installing pyproject-srpm-mac 100% |   1.2 MiB/s |   2.5 KiB |  00m00s
[152/155] Installing util-linux-0:2.40. 100% |  88.5 MiB/s |   3.7 MiB |  00m00s
[153/155] Installing authselect-0:1.5.0 100% |  38.6 MiB/s | 157.9 KiB |  00m00s
[154/155] Installing which-0:2.21-42.fc 100% |  40.2 MiB/s |  82.4 KiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[155/155] Installing info-0:7.1.1-1.fc4 100% | 121.2 KiB/s | 362.3 KiB |  00m03s
Warning: skipped PGP checks for 2 packages from repository: copr_base
Complete!
Finish: installing minimal buildroot with dnf5
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-0.3.6-1.fc41.x86_64
alternatives-1.30-1.fc41.x86_64
ansible-srpm-macros-1-16.fc41.noarch
audit-libs-4.0.2-1.fc41.x86_64
authselect-1.5.0-7.fc41.x86_64
authselect-libs-1.5.0-7.fc41.x86_64
basesystem-11-21.fc41.noarch
bash-5.2.32-2.fc42.x86_64
binutils-2.43.50-1.fc42.x86_64
build-reproducibility-srpm-macros-0.3.6-1.fc41.noarch
bzip2-1.0.8-19.fc41.x86_64
bzip2-libs-1.0.8-19.fc41.x86_64
ca-certificates-2024.2.69_v8.0.401-1.fc42.noarch
coreutils-9.5-9.fc42.x86_64
coreutils-common-9.5-9.fc42.x86_64
cpio-2.15-2.fc41.x86_64
cracklib-2.9.11-6.fc41.x86_64
crypto-policies-20240828-1.git5f66e81.fc42.noarch
curl-8.10.1-1.fc42.x86_64
cyrus-sasl-lib-2.1.28-27.fc41.x86_64
debugedit-5.0-17.fc41.x86_64
diffutils-3.10-8.fc41.x86_64
dwz-0.15-7.fc41.x86_64
ed-1.20.2-2.fc41.x86_64
efi-srpm-macros-5-12.fc41.noarch
elfutils-0.191-8.fc41.x86_64
elfutils-debuginfod-client-0.191-8.fc41.x86_64
elfutils-default-yama-scope-0.191-8.fc41.noarch
elfutils-libelf-0.191-8.fc41.x86_64
elfutils-libs-0.191-8.fc41.x86_64
fedora-gpg-keys-42-0.2.noarch
fedora-release-42-0.3.noarch
fedora-release-common-42-0.3.noarch
fedora-release-identity-basic-42-0.3.noarch
fedora-repos-42-0.2.noarch
fedora-repos-rawhide-42-0.2.noarch
file-5.45-7.fc41.x86_64
file-libs-5.45-7.fc41.x86_64
filesystem-3.18-29.fc42.x86_64
findutils-4.10.0-4.fc41.x86_64
fonts-srpm-macros-2.0.5-17.fc41.noarch
forge-srpm-macros-0.3.2-1.fc41.noarch
fpc-srpm-macros-1.3-13.fc41.noarch
gawk-5.3.0-4.fc41.x86_64
gdb-minimal-15.1-2.fc42.x86_64
gdbm-1.23-7.fc41.x86_64
gdbm-libs-1.23-7.fc41.x86_64
ghc-srpm-macros-1.9.2-1.fc42.noarch
glibc-2.40.9000-1.fc42.x86_64
glibc-common-2.40.9000-1.fc42.x86_64
glibc-gconv-extra-2.40.9000-1.fc42.x86_64
glibc-minimal-langpack-2.40.9000-1.fc42.x86_64
gmp-6.3.0-2.fc41.x86_64
gnat-srpm-macros-6-6.fc41.noarch
go-srpm-macros-3.6.0-3.fc41.noarch
gpg-pubkey-105ef944-65ca83d1
gpg-pubkey-31645531-66b6dccf
gpg-pubkey-e99d6ad1-64d2612c
grep-3.11-9.fc41.x86_64
gzip-1.13-2.fc41.x86_64
info-7.1.1-1.fc42.x86_64
jansson-2.13.1-10.fc41.x86_64
kernel-srpm-macros-1.0-24.fc41.noarch
keyutils-libs-1.6.3-4.fc41.x86_64
krb5-libs-1.21.3-2.fc41.x86_64
libacl-2.3.2-2.fc41.x86_64
libarchive-3.7.4-3.fc42.x86_64
libattr-2.5.2-4.fc41.x86_64
libblkid-2.40.2-8.fc42.x86_64
libbrotli-1.1.0-5.fc41.x86_64
libcap-2.70-4.fc41.x86_64
libcap-ng-0.8.5-3.fc41.x86_64
libcom_err-1.47.1-3.fc41.x86_64
libcurl-8.10.1-1.fc42.x86_64
libeconf-0.6.2-3.fc41.x86_64
libevent-2.1.12-14.fc41.x86_64
libfdisk-2.40.2-8.fc42.x86_64
libffi-3.4.6-3.fc42.x86_64
libgcc-14.2.1-3.fc42.x86_64
libgomp-14.2.1-3.fc42.x86_64
libidn2-2.3.7-2.fc41.x86_64
libmount-2.40.2-8.fc42.x86_64
libnghttp2-1.63.0-1.fc42.x86_64
libnsl2-2.0.1-2.fc41.x86_64
libpkgconf-2.3.0-1.fc42.x86_64
libpsl-0.21.5-4.fc41.x86_64
libpwquality-1.4.5-11.fc41.x86_64
libselinux-3.7-6.fc42.x86_64
libsemanage-3.7-3.fc42.x86_64
libsepol-3.7-3.fc42.x86_64
libsmartcols-2.40.2-8.fc42.x86_64
libssh-0.11.1-1.fc42.x86_64
libssh-config-0.11.1-1.fc42.noarch
libstdc++-14.2.1-3.fc42.x86_64
libtasn1-4.19.0-9.fc41.x86_64
libtirpc-1.3.5-0.fc41.x86_64
libtool-ltdl-2.4.7-12.fc41.x86_64
libunistring-1.1-8.fc41.x86_64
libuuid-2.40.2-8.fc42.x86_64
libverto-0.3.2-9.fc41.x86_64
libxcrypt-4.4.36-7.fc41.x86_64
libxml2-2.12.8-2.fc41.x86_64
libzstd-1.5.6-2.fc41.x86_64
lua-libs-5.4.6-6.fc41.x86_64
lua-srpm-macros-1-14.fc41.noarch
lz4-libs-1.10.0-1.fc41.x86_64
mpfr-4.2.1-5.fc41.x86_64
ncurses-base-6.5-2.20240629.fc41.noarch
ncurses-libs-6.5-2.20240629.fc41.x86_64
ocaml-srpm-macros-10-3.fc41.noarch
openblas-srpm-macros-2-18.fc41.noarch
openldap-2.6.8-5.fc41.x86_64
openssl-libs-3.2.2-8.fc42.x86_64
p11-kit-0.25.5-3.fc41.x86_64
p11-kit-trust-0.25.5-3.fc41.x86_64
package-notes-srpm-macros-0.5-12.fc41.noarch
pam-1.6.1-6.fc42.x86_64
pam-libs-1.6.1-6.fc42.x86_64
patch-2.7.6-25.fc41.x86_64
pcre2-10.44-1.fc41.1.x86_64
pcre2-syntax-10.44-1.fc41.1.noarch
perl-srpm-macros-1-56.fc41.noarch
pkgconf-2.3.0-1.fc42.x86_64
pkgconf-m4-2.3.0-1.fc42.noarch
pkgconf-pkg-config-2.3.0-1.fc42.x86_64
popt-1.19-7.fc41.x86_64
publicsuffix-list-dafsa-20240107-4.fc41.noarch
pyproject-srpm-macros-1.15.0-1.fc42.noarch
python-srpm-macros-3.13-3.fc41.noarch
qt5-srpm-macros-5.15.15-1.fc42.noarch
qt6-srpm-macros-6.7.2-3.fc41.noarch
readline-8.2-11.fc42.x86_64
redhat-rpm-config-295-1.fc42.noarch
rpm-4.19.94-1.fc42.x86_64
rpm-build-4.19.94-1.fc42.x86_64
rpm-build-libs-4.19.94-1.fc42.x86_64
rpm-libs-4.19.94-1.fc42.x86_64
rpm-sequoia-1.7.0-2.fc41.x86_64
rust-srpm-macros-26.3-3.fc42.noarch
sed-4.9-3.fc41.x86_64
setup-2.15.0-5.fc41.noarch
shadow-utils-4.16.0-4.fc42.x86_64
sqlite-libs-3.46.0-4.fc41.x86_64
systemd-libs-256.5-1.fc42.x86_64
tar-1.35-4.fc41.x86_64
unzip-6.0-64.fc41.x86_64
util-linux-2.40.2-8.fc42.x86_64
util-linux-core-2.40.2-8.fc42.x86_64
which-2.21-42.fc41.x86_64
xxhash-libs-0.8.2-3.fc41.x86_64
xz-5.6.2-2.fc41.x86_64
xz-libs-5.6.2-2.fc41.x86_64
zig-srpm-macros-1-3.fc41.noarch
zip-3.0-41.fc41.x86_64
zlib-ng-compat-2.2.2-1.fc42.x86_64
zstd-1.5.6-2.fc41.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1721174400
Wrote: /builddir/build/SRPMS/bowtie2-2.5.1-5.fc42.src.rpm
Finish: rpmbuild -bs
cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-rawhide-x86_64-1727276439.052334/root/var/log’: No such file or directory
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1727276439.052334/root/var/log/dnf5.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-a_h_yocn/bowtie2/bowtie2.spec) Config(child) 0 minutes 37 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/bowtie2-2.5.1-5.fc42.src.rpm)  Config(fedora-rawhide-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1727276439.052334/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1727276439.052334/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1727276439.052334/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.94-1.fc42.x86_64
  rpm-sequoia-1.7.0-2.fc41.x86_64
  dnf5-5.2.6.2-1.fc42.x86_64
  dnf5-plugins-5.2.6.2-1.fc42.x86_64
Finish: chroot init
Start: build phase for bowtie2-2.5.1-5.fc42.src.rpm
Start: build setup for bowtie2-2.5.1-5.fc42.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1721174400
Wrote: /builddir/build/SRPMS/bowtie2-2.5.1-5.fc42.src.rpm
Updating and loading repositories:
 fedora                                 100% | 872.6 KiB/s |  23.6 KiB |  00m00s
 Copr repository                        100% |  47.9 KiB/s |   1.5 KiB |  00m00s
 fedora                                 100% | 419.3 KiB/s | 472.5 KiB |  00m01s
Repositories loaded.
Package                 Arch   Version              Repository      Size
Installing:
 gcc-c++                x86_64 14.2.1-3.fc42        fedora      38.2 MiB
 help2man               noarch 1.49.3-6.fc41        fedora     415.6 KiB
 libasan                x86_64 14.2.1-3.fc42        fedora       1.6 MiB
 libubsan               x86_64 14.2.1-3.fc42        fedora     467.3 KiB
 make                   x86_64 1:4.4.1-8.fc41       fedora       1.8 MiB
 perl-Clone             x86_64 0.47-1.fc42          fedora      36.5 KiB
 perl-File-Which        noarch 1.27-12.fc41         fedora      30.4 KiB
 perl-FindBin           noarch 1.54-511.fc41        fedora       6.7 KiB
 perl-Sys-Hostname      x86_64 1.25-511.fc41        fedora      19.9 KiB
 perl-Test-Deep         noarch 1.204-6.fc41         fedora     264.1 KiB
 perl-generators        noarch 1.16-6.fc41          fedora      21.8 KiB
 perl-interpreter       x86_64 4:5.40.0-511.fc41    fedora     122.3 KiB
 perl-lib               x86_64 0.65-511.fc41        fedora       8.5 KiB
 python3                x86_64 3.13.0~rc2-3.fc42    fedora      31.8 KiB
 zlib-ng-compat-devel   x86_64 2.2.2-1.fc42         copr_base  106.8 KiB
Installing dependencies:
 annobin-docs           noarch 12.70-1.fc42         fedora      97.7 KiB
 annobin-plugin-gcc     x86_64 12.70-1.fc42         fedora     985.6 KiB
 cmake-filesystem       x86_64 3.28.3-7.fc41        fedora       0.0   B
 cpp                    x86_64 14.2.1-3.fc42        fedora      35.0 MiB
 expat                  x86_64 2.6.3-1.fc42         fedora     291.5 KiB
 gcc                    x86_64 14.2.1-3.fc42        fedora     104.4 MiB
 gcc-plugin-annobin     x86_64 14.2.1-3.fc42        fedora      61.1 KiB
 glibc-devel            x86_64 2.40.9000-1.fc42     fedora      37.8 KiB
 glibc-headers-x86      noarch 2.40.9000-1.fc42     fedora       2.2 MiB
 groff-base             x86_64 1.23.0-7.fc41        fedora       3.8 MiB
 kernel-headers         x86_64 6.11.0-63.fc42       fedora       6.4 MiB
 libb2                  x86_64 0.98.1-12.fc41       fedora      42.2 KiB
 libmpc                 x86_64 1.3.1-6.fc41         fedora     164.7 KiB
 libstdc++-devel        x86_64 14.2.1-3.fc42        fedora      15.4 MiB
 libxcrypt-devel        x86_64 4.4.36-7.fc41        fedora      30.3 KiB
 mpdecimal              x86_64 2.5.1-16.fc41        fedora     204.9 KiB
 ncurses                x86_64 6.5-2.20240629.fc41  fedora     627.3 KiB
 perl-AutoLoader        noarch 5.74-511.fc41        fedora      20.5 KiB
 perl-B                 x86_64 1.89-511.fc41        fedora     498.0 KiB
 perl-Carp              noarch 1.54-511.fc41        fedora      46.6 KiB
 perl-Class-Struct      noarch 0.68-511.fc41        fedora      25.4 KiB
 perl-Data-Dumper       x86_64 2.189-512.fc41       fedora     111.7 KiB
 perl-Digest            noarch 1.20-511.fc41        fedora      35.3 KiB
 perl-Digest-MD5        x86_64 2.59-5.fc41          fedora      59.8 KiB
 perl-DynaLoader        x86_64 1.56-511.fc41        fedora      32.1 KiB
 perl-Encode            x86_64 4:3.21-511.fc41      fedora       4.7 MiB
 perl-Errno             x86_64 1.38-511.fc41        fedora       8.4 KiB
 perl-Exporter          noarch 5.78-511.fc41        fedora      54.3 KiB
 perl-Fcntl             x86_64 1.18-511.fc41        fedora      49.0 KiB
 perl-Fedora-VSP        noarch 0.001-35.fc41        fedora      39.7 KiB
 perl-File-Basename     noarch 2.86-511.fc41        fedora      14.0 KiB
 perl-File-Path         noarch 2.18-511.fc41        fedora      63.5 KiB
 perl-File-Temp         noarch 1:0.231.100-511.fc41 fedora     162.3 KiB
 perl-File-stat         noarch 1.14-511.fc41        fedora      12.5 KiB
 perl-FileHandle        noarch 2.05-511.fc41        fedora       9.3 KiB
 perl-Getopt-Long       noarch 1:2.58-2.fc41        fedora     144.5 KiB
 perl-Getopt-Std        noarch 1.14-511.fc41        fedora      11.2 KiB
 perl-HTTP-Tiny         noarch 0.088-512.fc41       fedora     152.2 KiB
 perl-IO                x86_64 1.55-511.fc41        fedora     151.1 KiB
 perl-IO-Socket-IP      noarch 0.42-512.fc41        fedora      98.7 KiB
 perl-IO-Socket-SSL     noarch 2.089-1.fc42         fedora     703.3 KiB
 perl-IPC-Open3         noarch 1.22-511.fc41        fedora      22.5 KiB
 perl-JSON-PP           noarch 1:4.16-512.fc41      fedora     141.8 KiB
 perl-MIME-Base32       noarch 1.303-21.fc41        fedora      30.7 KiB
 perl-MIME-Base64       x86_64 3.16-511.fc41        fedora      46.1 KiB
 perl-Math-BigInt       noarch 1:2.0030.03-3.fc41   fedora     957.7 KiB
 perl-Math-Complex      noarch 1.62-511.fc41        fedora      85.0 KiB
 perl-Mozilla-CA        noarch 20240730-1.fc41      fedora       9.8 KiB
 perl-Net-SSLeay        x86_64 1.94-7.fc41          fedora       1.3 MiB
 perl-Object-HashBase   noarch 0.015-1.fc42         fedora      54.8 KiB
 perl-POSIX             x86_64 2.20-511.fc41        fedora     235.1 KiB
 perl-PathTools         x86_64 3.91-511.fc41        fedora     180.0 KiB
 perl-Pod-Escapes       noarch 1:1.07-511.fc41      fedora      24.9 KiB
 perl-Pod-Perldoc       noarch 3.28.01-512.fc41     fedora     163.7 KiB
 perl-Pod-Simple        noarch 1:3.45-511.fc41      fedora     560.9 KiB
 perl-Pod-Usage         noarch 4:2.03-511.fc41      fedora      84.8 KiB
 perl-Scalar-List-Utils x86_64 5:1.66-1.fc42        fedora     146.6 KiB
 perl-SelectSaver       noarch 1.02-511.fc41        fedora       2.2 KiB
 perl-Socket            x86_64 4:2.038-511.fc41     fedora     124.0 KiB
 perl-Storable          x86_64 1:3.32-511.fc41      fedora     232.4 KiB
 perl-Symbol            noarch 1.09-511.fc41        fedora       6.8 KiB
 perl-Term-ANSIColor    noarch 5.01-512.fc41        fedora      97.5 KiB
 perl-Term-Cap          noarch 1.18-511.fc41        fedora      29.3 KiB
 perl-Term-Table        noarch 0.022-1.fc42         fedora      60.6 KiB
 perl-Test-Simple       noarch 3:1.302204-1.fc42    fedora       1.7 MiB
 perl-Text-ParseWords   noarch 3.31-511.fc41        fedora      13.6 KiB
 perl-Text-Tabs+Wrap    noarch 2024.001-511.fc41    fedora      22.6 KiB
 perl-Time-HiRes        x86_64 4:1.9777-511.fc41    fedora     119.9 KiB
 perl-Time-Local        noarch 2:1.350-511.fc41     fedora      69.0 KiB
 perl-URI               noarch 5.29-1.fc42          fedora     251.9 KiB
 perl-base              noarch 2.27-511.fc41        fedora      12.5 KiB
 perl-constant          noarch 1.33-512.fc41        fedora      26.2 KiB
 perl-if                noarch 0.61.000-511.fc41    fedora       5.8 KiB
 perl-libnet            noarch 3.15-512.fc41        fedora     289.4 KiB
 perl-libs              x86_64 4:5.40.0-511.fc41    fedora       9.9 MiB
 perl-locale            noarch 1.12-511.fc41        fedora       6.5 KiB
 perl-macros            noarch 4:5.40.0-511.fc41    fedora       5.5 KiB
 perl-mro               x86_64 1.29-511.fc41        fedora      45.6 KiB
 perl-overload          noarch 1.37-511.fc41        fedora      71.5 KiB
 perl-overloading       noarch 0.02-511.fc41        fedora       4.8 KiB
 perl-parent            noarch 1:0.242-1.fc42       fedora      10.0 KiB
 perl-podlators         noarch 1:6.0.2-2.fc41       fedora     317.5 KiB
 perl-threads           x86_64 1:2.40-511.fc41      fedora     115.1 KiB
 perl-vars              noarch 1.05-511.fc41        fedora       3.9 KiB
 python-pip-wheel       noarch 24.2-2.fc42          fedora       1.2 MiB
 python3-libs           x86_64 3.13.0~rc2-3.fc42    fedora      40.3 MiB
 tzdata                 noarch 2024a-9.fc41         fedora       1.7 MiB

Transaction Summary:
 Installing:       102 packages

Total size of inbound packages is 92 MiB. Need to download 92 MiB.
After this operation, 281 MiB extra will be used (install 281 MiB, remove 0 B).
[  1/102] perl-Clone-0:0.47-1.fc42.x86_ 100% |  88.0 KiB/s |  22.3 KiB |  00m00s
[  2/102] help2man-0:1.49.3-6.fc41.noar 100% | 485.5 KiB/s | 227.2 KiB |  00m00s
[  3/102] perl-File-Which-0:1.27-12.fc4 100% |  78.6 KiB/s |  21.7 KiB |  00m00s
[  4/102] make-1:4.4.1-8.fc41.x86_64    100% |   1.1 MiB/s | 586.1 KiB |  00m01s
[  5/102] perl-FindBin-0:1.54-511.fc41. 100% |  71.6 KiB/s |  14.2 KiB |  00m00s
[  6/102] perl-Test-Deep-0:1.204-6.fc41 100% | 817.7 KiB/s | 118.6 KiB |  00m00s
[  7/102] perl-Sys-Hostname-0:1.25-511. 100% | 103.7 KiB/s |  17.2 KiB |  00m00s
[  8/102] perl-lib-0:0.65-511.fc41.x86_ 100% | 213.0 KiB/s |  14.9 KiB |  00m00s
[  9/102] perl-generators-0:1.16-6.fc41 100% | 136.0 KiB/s |  16.5 KiB |  00m00s
[ 10/102] perl-interpreter-4:5.40.0-511 100% | 325.7 KiB/s |  72.3 KiB |  00m00s
[ 11/102] libasan-0:14.2.1-3.fc42.x86_6 100% |   3.2 MiB/s | 514.2 KiB |  00m00s
[ 12/102] python3-0:3.13.0~rc2-3.fc42.x 100% | 153.0 KiB/s |  27.7 KiB |  00m00s
[ 13/102] zlib-ng-compat-devel-0:2.2.2- 100% |   1.0 MiB/s |  38.7 KiB |  00m00s
[ 14/102] perl-Getopt-Long-1:2.58-2.fc4 100% | 887.4 KiB/s |  63.9 KiB |  00m00s
[ 15/102] libubsan-0:14.2.1-3.fc42.x86_ 100% | 634.1 KiB/s | 223.2 KiB |  00m00s
[ 16/102] perl-POSIX-0:2.20-511.fc41.x8 100% |   1.3 MiB/s |  97.0 KiB |  00m00s
[ 17/102] perl-Text-ParseWords-0:3.31-5 100% | 233.5 KiB/s |  16.6 KiB |  00m00s
[ 18/102] perl-Text-Tabs+Wrap-0:2024.00 100% | 321.3 KiB/s |  21.9 KiB |  00m00s
[ 19/102] perl-AutoLoader-0:5.74-511.fc 100% | 294.4 KiB/s |  21.2 KiB |  00m00s
[ 20/102] perl-Exporter-0:5.78-511.fc41 100% | 448.0 KiB/s |  30.9 KiB |  00m00s
[ 21/102] gcc-c++-0:14.2.1-3.fc42.x86_6 100% |  18.8 MiB/s |  14.2 MiB |  00m01s
[ 22/102] perl-PathTools-0:3.91-511.fc4 100% |   1.2 MiB/s |  87.4 KiB |  00m00s
[ 23/102] perl-base-0:2.27-511.fc41.noa 100% | 237.8 KiB/s |  16.2 KiB |  00m00s
[ 24/102] perl-constant-0:1.33-512.fc41 100% | 338.7 KiB/s |  23.0 KiB |  00m00s
[ 25/102] perl-Carp-0:1.54-511.fc41.noa 100% | 418.7 KiB/s |  28.9 KiB |  00m00s
[ 26/102] perl-File-Basename-0:2.86-511 100% | 251.8 KiB/s |  17.1 KiB |  00m00s
[ 27/102] perl-Scalar-List-Utils-5:1.66 100% | 768.6 KiB/s |  72.2 KiB |  00m00s
[ 28/102] perl-libs-4:5.40.0-511.fc41.x 100% |   7.4 MiB/s |   2.3 MiB |  00m00s
[ 29/102] perl-overload-0:1.37-511.fc41 100% | 649.9 KiB/s |  45.5 KiB |  00m00s
[ 30/102] perl-Fedora-VSP-0:0.001-35.fc 100% | 118.7 KiB/s |  23.0 KiB |  00m00s
[ 31/102] perl-macros-4:5.40.0-511.fc41 100% |  88.4 KiB/s |  12.3 KiB |  00m00s
[ 32/102] perl-Test-Simple-3:1.302204-1 100% |   3.1 MiB/s | 863.0 KiB |  00m00s
[ 33/102] libmpc-0:1.3.1-6.fc41.x86_64  100% |   1.0 MiB/s |  71.1 KiB |  00m00s
[ 34/102] cmake-filesystem-0:3.28.3-7.f 100% | 264.5 KiB/s |  18.2 KiB |  00m00s
[ 35/102] perl-Pod-Usage-4:2.03-511.fc4 100% | 579.8 KiB/s |  40.0 KiB |  00m00s
[ 36/102] perl-Fcntl-0:1.18-511.fc41.x8 100% | 419.3 KiB/s |  29.8 KiB |  00m00s
[ 37/102] perl-locale-0:1.12-511.fc41.n 100% | 183.5 KiB/s |  13.6 KiB |  00m00s
[ 38/102] perl-DynaLoader-0:1.56-511.fc 100% | 132.7 KiB/s |  26.0 KiB |  00m00s
[ 39/102] perl-Errno-0:1.38-511.fc41.x8 100% | 167.6 KiB/s |  14.9 KiB |  00m00s
[ 40/102] python3-libs-0:3.13.0~rc2-3.f 100% |  13.3 MiB/s |   9.1 MiB |  00m01s
[ 41/102] perl-B-0:1.89-511.fc41.x86_64 100% |   2.4 MiB/s | 176.3 KiB |  00m00s
[ 42/102] perl-Data-Dumper-0:2.189-512. 100% | 804.9 KiB/s |  56.3 KiB |  00m00s
[ 43/102] perl-File-Temp-1:0.231.100-51 100% | 821.1 KiB/s |  59.1 KiB |  00m00s
[ 44/102] perl-IO-0:1.55-511.fc41.x86_6 100% |   1.0 MiB/s |  81.9 KiB |  00m00s
[ 45/102] perl-Storable-1:3.32-511.fc41 100% |   1.4 MiB/s |  98.4 KiB |  00m00s
[ 46/102] perl-Symbol-0:1.09-511.fc41.n 100% | 208.2 KiB/s |  14.2 KiB |  00m00s
[ 47/102] perl-Term-ANSIColor-0:5.01-51 100% | 701.3 KiB/s |  47.7 KiB |  00m00s
[ 48/102] perl-JSON-PP-1:4.16-512.fc41. 100% | 187.9 KiB/s |  66.1 KiB |  00m00s
[ 49/102] perl-Term-Table-0:0.022-1.fc4 100% | 438.7 KiB/s |  34.7 KiB |  00m00s
[ 50/102] perl-mro-0:1.29-511.fc41.x86_ 100% | 439.6 KiB/s |  29.9 KiB |  00m00s
[ 51/102] perl-Time-HiRes-4:1.9777-511. 100% | 531.0 KiB/s |  57.3 KiB |  00m00s
[ 52/102] gcc-0:14.2.1-3.fc42.x86_64    100% |  28.3 MiB/s |  37.0 MiB |  00m01s
[ 53/102] perl-threads-1:2.40-511.fc41. 100% | 715.8 KiB/s |  58.0 KiB |  00m00s
[ 54/102] perl-vars-0:1.05-511.fc41.noa 100% | 190.5 KiB/s |  13.0 KiB |  00m00s
[ 55/102] perl-overloading-0:0.02-511.f 100% | 189.2 KiB/s |  12.9 KiB |  00m00s
[ 56/102] expat-0:2.6.3-1.fc42.x86_64   100% |   1.6 MiB/s | 114.1 KiB |  00m00s
[ 57/102] libb2-0:0.98.1-12.fc41.x86_64 100% | 282.2 KiB/s |  25.7 KiB |  00m00s
[ 58/102] mpdecimal-0:2.5.1-16.fc41.x86 100% |   1.3 MiB/s |  89.0 KiB |  00m00s
[ 59/102] python-pip-wheel-0:24.2-2.fc4 100% |  13.5 MiB/s |   1.2 MiB |  00m00s
[ 60/102] tzdata-0:2024a-9.fc41.noarch  100% |   7.4 MiB/s | 714.7 KiB |  00m00s
[ 61/102] perl-Pod-Perldoc-0:3.28.01-51 100% |   1.2 MiB/s |  86.1 KiB |  00m00s
[ 62/102] perl-podlators-1:6.0.2-2.fc41 100% |   1.8 MiB/s | 128.8 KiB |  00m00s
[ 63/102] cpp-0:14.2.1-3.fc42.x86_64    100% |  34.6 MiB/s |  11.9 MiB |  00m00s
[ 64/102] perl-if-0:0.61.000-511.fc41.n 100% | 205.3 KiB/s |  14.0 KiB |  00m00s
[ 65/102] perl-File-Path-0:2.18-511.fc4 100% | 518.5 KiB/s |  35.3 KiB |  00m00s
[ 66/102] perl-parent-1:0.242-1.fc42.no 100% | 220.0 KiB/s |  15.0 KiB |  00m00s
[ 67/102] perl-File-stat-0:1.14-511.fc4 100% | 250.1 KiB/s |  17.0 KiB |  00m00s
[ 68/102] perl-SelectSaver-0:1.02-511.f 100% | 171.8 KiB/s |  11.7 KiB |  00m00s
[ 69/102] perl-Socket-4:2.038-511.fc41. 100% | 806.3 KiB/s |  54.8 KiB |  00m00s
[ 70/102] perl-Object-HashBase-0:0.015- 100% | 366.9 KiB/s |  28.6 KiB |  00m00s
[ 71/102] perl-Math-BigInt-1:2.0030.03- 100% |   2.3 MiB/s | 225.7 KiB |  00m00s
[ 72/102] groff-base-0:1.23.0-7.fc41.x8 100% |  11.8 MiB/s |   1.1 MiB |  00m00s
[ 73/102] perl-HTTP-Tiny-0:0.088-512.fc 100% | 820.8 KiB/s |  55.8 KiB |  00m00s
[ 74/102] perl-IPC-Open3-0:1.22-511.fc4 100% | 320.9 KiB/s |  21.8 KiB |  00m00s
[ 75/102] perl-Pod-Simple-1:3.45-511.fc 100% |   3.0 MiB/s | 219.0 KiB |  00m00s
[ 76/102] perl-Term-Cap-0:1.18-511.fc41 100% | 324.5 KiB/s |  22.1 KiB |  00m00s
[ 77/102] perl-Class-Struct-0:0.68-511. 100% | 323.8 KiB/s |  22.0 KiB |  00m00s
[ 78/102] perl-IO-Socket-SSL-0:2.089-1. 100% |   3.1 MiB/s | 231.2 KiB |  00m00s
[ 79/102] perl-Mozilla-CA-0:20240730-1. 100% | 209.7 KiB/s |  14.3 KiB |  00m00s
[ 80/102] perl-Math-Complex-0:1.62-511. 100% | 222.4 KiB/s |  46.0 KiB |  00m00s
[ 81/102] perl-MIME-Base64-0:3.16-511.f 100% | 184.8 KiB/s |  29.9 KiB |  00m00s
[ 82/102] perl-Net-SSLeay-0:1.94-7.fc41 100% |   4.8 MiB/s | 375.7 KiB |  00m00s
[ 83/102] perl-Time-Local-2:1.350-511.f 100% | 500.4 KiB/s |  34.5 KiB |  00m00s
[ 84/102] perl-Pod-Escapes-1:1.07-511.f 100% | 291.4 KiB/s |  19.8 KiB |  00m00s
[ 85/102] ncurses-0:6.5-2.20240629.fc41 100% |   5.2 MiB/s | 423.8 KiB |  00m00s
[ 86/102] perl-IO-Socket-IP-0:0.42-512. 100% | 435.6 KiB/s |  41.8 KiB |  00m00s
[ 87/102] perl-URI-0:5.29-1.fc42.noarch 100% |   1.4 MiB/s | 137.7 KiB |  00m00s
[ 88/102] perl-MIME-Base32-0:1.303-21.f 100% | 301.1 KiB/s |  20.5 KiB |  00m00s
[ 89/102] perl-libnet-0:3.15-512.fc41.n 100% |   1.8 MiB/s | 128.5 KiB |  00m00s
[ 90/102] perl-Digest-MD5-0:2.59-5.fc41 100% | 521.9 KiB/s |  36.0 KiB |  00m00s
[ 91/102] perl-FileHandle-0:2.05-511.fc 100% | 227.3 KiB/s |  15.5 KiB |  00m00s
[ 92/102] perl-Digest-0:1.20-511.fc41.n 100% | 360.9 KiB/s |  24.9 KiB |  00m00s
[ 93/102] perl-Encode-4:3.21-511.fc41.x 100% |  11.7 MiB/s |   1.1 MiB |  00m00s
[ 94/102] perl-Getopt-Std-0:1.14-511.fc 100% | 230.1 KiB/s |  15.6 KiB |  00m00s
[ 95/102] glibc-devel-0:2.40.9000-1.fc4 100% |   1.8 MiB/s | 135.6 KiB |  00m00s
[ 96/102] glibc-headers-x86-0:2.40.9000 100% |   6.5 MiB/s | 627.7 KiB |  00m00s
[ 97/102] libstdc++-devel-0:14.2.1-3.fc 100% |  21.2 MiB/s |   2.8 MiB |  00m00s
[ 98/102] libxcrypt-devel-0:4.4.36-7.fc 100% | 424.4 KiB/s |  28.9 KiB |  00m00s
[ 99/102] annobin-plugin-gcc-0:12.70-1. 100% |   9.5 MiB/s | 971.7 KiB |  00m00s
[100/102] kernel-headers-0:6.11.0-63.fc 100% |  15.0 MiB/s |   1.6 MiB |  00m00s
[101/102] gcc-plugin-annobin-0:14.2.1-3 100% | 799.5 KiB/s |  55.2 KiB |  00m00s
[102/102] annobin-docs-0:12.70-1.fc42.n 100% | 928.9 KiB/s |  92.0 KiB |  00m00s
--------------------------------------------------------------------------------
[102/102] Total                         100% |  19.3 MiB/s |  91.8 MiB |  00m05s
Running transaction
[  1/104] Verify package files          100% | 321.0   B/s | 102.0   B |  00m00s
[  2/104] Prepare transaction           100% |   1.1 KiB/s | 102.0   B |  00m00s
[  3/104] Installing libmpc-0:1.3.1-6.f 100% |  81.1 MiB/s | 166.2 KiB |  00m00s
[  4/104] Installing cpp-0:14.2.1-3.fc4 100% | 275.6 MiB/s |  35.0 MiB |  00m00s
[  5/104] Installing annobin-docs-0:12. 100% |  24.1 MiB/s |  98.8 KiB |  00m00s
[  6/104] Installing kernel-headers-0:6 100% | 107.3 MiB/s |   6.5 MiB |  00m00s
[  7/104] Installing glibc-headers-x86- 100% |  91.4 MiB/s |   2.3 MiB |  00m00s
[  8/104] Installing libxcrypt-devel-0: 100% |  15.9 MiB/s |  32.6 KiB |  00m00s
[  9/104] Installing glibc-devel-0:2.40 100% |  10.1 MiB/s |  41.5 KiB |  00m00s
[ 10/104] Installing libstdc++-devel-0: 100% | 210.2 MiB/s |  15.6 MiB |  00m00s
[ 11/104] Installing ncurses-0:6.5-2.20 100% |  32.6 MiB/s | 633.9 KiB |  00m00s
[ 12/104] Installing groff-base-0:1.23. 100% | 107.6 MiB/s |   3.9 MiB |  00m00s
[ 13/104] Installing perl-Digest-0:1.20 100% |  36.2 MiB/s |  37.1 KiB |  00m00s
[ 14/104] Installing perl-B-0:1.89-511. 100% | 122.4 MiB/s | 501.3 KiB |  00m00s
[ 15/104] Installing perl-FileHandle-0: 100% |   0.0   B/s |   9.8 KiB |  00m00s
[ 16/104] Installing perl-Digest-MD5-0: 100% |  30.1 MiB/s |  61.7 KiB |  00m00s
[ 17/104] Installing perl-Data-Dumper-0 100% |  55.5 MiB/s | 113.6 KiB |  00m00s
[ 18/104] Installing perl-MIME-Base32-0 100% |  31.4 MiB/s |  32.2 KiB |  00m00s
[ 19/104] Installing perl-libnet-0:3.15 100% |  95.9 MiB/s | 294.7 KiB |  00m00s
[ 20/104] Installing perl-AutoLoader-0: 100% |   0.0   B/s |  20.9 KiB |  00m00s
[ 21/104] Installing perl-IO-Socket-IP- 100% |  49.1 MiB/s | 100.5 KiB |  00m00s
[ 22/104] Installing perl-URI-0:5.29-1. 100% |  51.5 MiB/s | 263.8 KiB |  00m00s
[ 23/104] Installing perl-Text-Tabs+Wra 100% |  23.3 MiB/s |  23.9 KiB |  00m00s
[ 24/104] Installing perl-locale-0:1.12 100% |   0.0   B/s |   6.9 KiB |  00m00s
[ 25/104] Installing perl-if-0:0.61.000 100% |   0.0   B/s |   6.2 KiB |  00m00s
[ 26/104] Installing perl-File-Path-0:2 100% |  63.0 MiB/s |  64.5 KiB |  00m00s
[ 27/104] Installing perl-Mozilla-CA-0: 100% |  10.6 MiB/s |  10.8 KiB |  00m00s
[ 28/104] Installing perl-Net-SSLeay-0: 100% | 136.3 MiB/s |   1.4 MiB |  00m00s
[ 29/104] Installing perl-Time-Local-2: 100% |  68.9 MiB/s |  70.6 KiB |  00m00s
[ 30/104] Installing perl-Pod-Escapes-1 100% |  25.3 MiB/s |  25.9 KiB |  00m00s
[ 31/104] Installing perl-IO-Socket-SSL 100% | 172.7 MiB/s | 707.4 KiB |  00m00s
[ 32/104] Installing perl-POSIX-0:2.20- 100% | 115.4 MiB/s | 236.4 KiB |  00m00s
[ 33/104] Installing perl-Term-ANSIColo 100% |  96.9 MiB/s |  99.2 KiB |  00m00s
[ 34/104] Installing perl-Term-Cap-0:1. 100% |  29.9 MiB/s |  30.6 KiB |  00m00s
[ 35/104] Installing perl-File-Temp-1:0 100% | 160.2 MiB/s | 164.1 KiB |  00m00s
[ 36/104] Installing perl-IPC-Open3-0:1 100% |  22.7 MiB/s |  23.3 KiB |  00m00s
[ 37/104] Installing perl-Class-Struct- 100% |  25.3 MiB/s |  25.9 KiB |  00m00s
[ 38/104] Installing perl-Pod-Simple-1: 100% | 139.3 MiB/s | 570.5 KiB |  00m00s
[ 39/104] Installing perl-HTTP-Tiny-0:0 100% |  75.3 MiB/s | 154.2 KiB |  00m00s
[ 40/104] Installing perl-Symbol-0:1.09 100% |   0.0   B/s |   7.2 KiB |  00m00s
[ 41/104] Installing perl-SelectSaver-0 100% |   0.0   B/s |   2.6 KiB |  00m00s
[ 42/104] Installing perl-Socket-4:2.03 100% |  61.6 MiB/s | 126.1 KiB |  00m00s
[ 43/104] Installing perl-File-stat-0:1 100% |  12.7 MiB/s |  13.1 KiB |  00m00s
[ 44/104] Installing perl-podlators-1:6 100% | 104.6 MiB/s | 321.4 KiB |  00m00s
[ 45/104] Installing perl-Pod-Perldoc-0 100% |  82.6 MiB/s | 169.3 KiB |  00m00s
[ 46/104] Installing perl-Text-ParseWor 100% |  14.2 MiB/s |  14.6 KiB |  00m00s
[ 47/104] Installing perl-base-0:2.27-5 100% |   0.0   B/s |  12.9 KiB |  00m00s
[ 48/104] Installing perl-Fcntl-0:1.18- 100% |  48.9 MiB/s |  50.1 KiB |  00m00s
[ 49/104] Installing perl-mro-0:1.29-51 100% |  45.6 MiB/s |  46.7 KiB |  00m00s
[ 50/104] Installing perl-overloading-0 100% |   5.4 MiB/s |   5.5 KiB |  00m00s
[ 51/104] Installing perl-IO-0:1.55-511 100% |  75.8 MiB/s | 155.3 KiB |  00m00s
[ 52/104] Installing perl-Pod-Usage-4:2 100% |  84.3 MiB/s |  86.3 KiB |  00m00s
[ 53/104] Installing perl-constant-0:1. 100% |  26.7 MiB/s |  27.4 KiB |  00m00s
[ 54/104] Installing perl-File-Basename 100% |   0.0   B/s |  14.6 KiB |  00m00s
[ 55/104] Installing perl-Scalar-List-U 100% |  48.8 MiB/s | 149.9 KiB |  00m00s
[ 56/104] Installing perl-Errno-0:1.38- 100% |   8.6 MiB/s |   8.8 KiB |  00m00s
[ 57/104] Installing perl-vars-0:1.05-5 100% |   0.0   B/s |   4.3 KiB |  00m00s
[ 58/104] Installing perl-overload-0:1. 100% |  70.3 MiB/s |  71.9 KiB |  00m00s
[ 59/104] Installing perl-parent-1:0.24 100% |  10.5 MiB/s |  10.7 KiB |  00m00s
[ 60/104] Installing perl-Storable-1:3. 100% | 114.3 MiB/s | 234.0 KiB |  00m00s
[ 61/104] Installing perl-MIME-Base64-0 100% |  23.6 MiB/s |  48.4 KiB |  00m00s
[ 62/104] Installing perl-Getopt-Std-0: 100% |  11.5 MiB/s |  11.7 KiB |  00m00s
[ 63/104] Installing perl-Getopt-Long-1 100% |  71.9 MiB/s | 147.2 KiB |  00m00s
[ 64/104] Installing perl-Exporter-0:5. 100% |  54.3 MiB/s |  55.6 KiB |  00m00s
[ 65/104] Installing perl-Carp-0:1.54-5 100% |  46.6 MiB/s |  47.7 KiB |  00m00s
[ 66/104] Installing perl-PathTools-0:3 100% |  60.1 MiB/s | 184.6 KiB |  00m00s
[ 67/104] Installing perl-DynaLoader-0: 100% |  31.7 MiB/s |  32.5 KiB |  00m00s
[ 68/104] Installing perl-Encode-4:3.21 100% | 214.5 MiB/s |   4.7 MiB |  00m00s
[ 69/104] Installing perl-libs-4:5.40.0 100% | 153.2 MiB/s |  10.0 MiB |  00m00s
[ 70/104] Installing perl-interpreter-4 100% |  60.5 MiB/s | 124.0 KiB |  00m00s
[ 71/104] Installing perl-macros-4:5.40 100% |   0.0   B/s |   5.8 KiB |  00m00s
[ 72/104] Installing perl-Fedora-VSP-0: 100% |  39.6 MiB/s |  40.6 KiB |  00m00s
[ 73/104] Installing perl-Time-HiRes-4: 100% |  59.5 MiB/s | 121.9 KiB |  00m00s
[ 74/104] Installing perl-threads-1:2.4 100% |  57.2 MiB/s | 117.2 KiB |  00m00s
[ 75/104] Installing perl-Object-HashBa 100% |  54.9 MiB/s |  56.2 KiB |  00m00s
[ 76/104] Installing perl-Term-Table-0: 100% |  31.0 MiB/s |  63.4 KiB |  00m00s
[ 77/104] Installing perl-Math-Complex- 100% |  83.8 MiB/s |  85.8 KiB |  00m00s
[ 78/104] Installing perl-Math-BigInt-1 100% | 234.8 MiB/s | 961.8 KiB |  00m00s
[ 79/104] Installing perl-JSON-PP-1:4.1 100% |  46.7 MiB/s | 143.6 KiB |  00m00s
[ 80/104] Installing perl-Test-Simple-3 100% |  61.2 MiB/s |   1.8 MiB |  00m00s
[ 81/104] Installing tzdata-0:2024a-9.f 100% |  27.0 MiB/s |   1.9 MiB |  00m00s
[ 82/104] Installing python-pip-wheel-0 100% | 413.9 MiB/s |   1.2 MiB |  00m00s
[ 83/104] Installing mpdecimal-0:2.5.1- 100% | 201.2 MiB/s | 206.0 KiB |  00m00s
[ 84/104] Installing libb2-0:0.98.1-12. 100% |  42.3 MiB/s |  43.3 KiB |  00m00s
[ 85/104] Installing expat-0:2.6.3-1.fc 100% |  41.0 MiB/s | 293.6 KiB |  00m00s
[ 86/104] Installing python3-libs-0:3.1 100% | 202.5 MiB/s |  40.7 MiB |  00m00s
[ 87/104] Installing cmake-filesystem-0 100% |   2.3 MiB/s |   7.1 KiB |  00m00s
[ 88/104] Installing make-1:4.4.1-8.fc4 100% | 163.7 MiB/s |   1.8 MiB |  00m00s
[ 89/104] Installing gcc-0:14.2.1-3.fc4 100% | 300.0 MiB/s | 104.4 MiB |  00m00s
[ 90/104] Installing gcc-c++-0:14.2.1-3 100% | 282.7 MiB/s |  38.2 MiB |  00m00s
[ 91/104] Installing annobin-plugin-gcc 100% |  34.4 MiB/s | 987.3 KiB |  00m00s
[ 92/104] Installing gcc-plugin-annobin 100% |   2.0 MiB/s |  62.7 KiB |  00m00s
[ 93/104] Installing zlib-ng-compat-dev 100% | 105.8 MiB/s | 108.3 KiB |  00m00s
[ 94/104] Installing python3-0:3.13.0~r 100% |  32.8 MiB/s |  33.6 KiB |  00m00s
[ 95/104] Installing perl-Test-Deep-0:1 100% |  45.4 MiB/s | 279.2 KiB |  00m00s
[ 96/104] Installing perl-generators-0: 100% |  22.6 MiB/s |  23.2 KiB |  00m00s
[ 97/104] Installing help2man-0:1.49.3- 100% |  59.3 MiB/s | 425.4 KiB |  00m00s
[ 98/104] Installing perl-Clone-0:0.47- 100% |  37.3 MiB/s |  38.2 KiB |  00m00s
[ 99/104] Installing perl-File-Which-0: 100% |  30.7 MiB/s |  31.4 KiB |  00m00s
[100/104] Installing perl-FindBin-0:1.5 100% |   0.0   B/s |   7.1 KiB |  00m00s
[101/104] Installing perl-Sys-Hostname- 100% |  20.8 MiB/s |  21.3 KiB |  00m00s
[102/104] Installing perl-lib-0:0.65-51 100% |   8.7 MiB/s |   8.9 KiB |  00m00s
[103/104] Installing libubsan-0:14.2.1- 100% | 228.6 MiB/s | 468.1 KiB |  00m00s
warning: posix.fork(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.wait(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
warning: posix.exec(): .fork(), .exec(), .wait() and .redirect2null() are deprecated, use rpm.spawn() or rpm.execute() instead
[104/104] Installing libasan-0:14.2.1-3 100% |   5.7 MiB/s |   1.6 MiB |  00m00s
Warning: skipped PGP checks for 1 package from repository: copr_base
Complete!
Finish: build setup for bowtie2-2.5.1-5.fc42.src.rpm
Start: rpmbuild bowtie2-2.5.1-5.fc42.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1721174400
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.6CGFDE
+ umask 022
+ cd /builddir/build/BUILD/bowtie2-2.5.1-build
+ test -d /builddir/build/BUILD/bowtie2-2.5.1-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bowtie2-2.5.1-build
+ /usr/bin/rm -rf /builddir/build/BUILD/bowtie2-2.5.1-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build/SPECPARTS
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.415yCY
+ umask 022
+ cd /builddir/build/BUILD/bowtie2-2.5.1-build
+ cd /builddir/build/BUILD/bowtie2-2.5.1-build
+ rm -rf bowtie2-2.5.1
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/v2.5.1.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bowtie2-2.5.1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ rm -rf third_party
+ sed -e 's/“/"/g' -e 's/”/"/g' -i processor_support.h
+ sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' bowtie2
+ for file in bowtie2-{build,inspect}
+ sed -i '1s|/usr/bin/env python3|/usr/bin/python3|' bowtie2-build
+ for file in bowtie2-{build,inspect}
+ sed -i '1s|/usr/bin/env python3|/usr/bin/python3|' bowtie2-inspect
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.ihP1zu
+ umask 022
+ cd /builddir/build/BUILD/bowtie2-2.5.1-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bowtie2-2.5.1
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ /usr/bin/make -O -j2 V=1 VERBOSE=1 all
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	-I third_party \
	-o bowtie2-build-s bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lpthread -lz
In file included from bt2_idx.h:60,
                 from bt2_build.cpp:28:
In member function ‘ProcessorSupport::POPCNTenabled()’,
    inlined from ‘Ebwt::Ebwt<S2bDnaString>(S2bDnaString, bool, int, int, int, int, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, unsigned int, unsigned int, unsigned int, int, EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned int, RefReadInParams const&, unsigned int, int, bool, bool, bool, bool, bool)’ at bt2_idx.h:669:43:
processor_support.h:55:13: warning: ‘MEM[(unsigned int *)&regs + 8B]’ may be used uninitialized [-Wmaybe-uninitialized]
   55 |         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In member function ‘Ebwt::Ebwt<S2bDnaString>(S2bDnaString, bool, int, int, int, int, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, unsigned int, unsigned int, unsigned int, int, EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned int, RefReadInParams const&, unsigned int, int, bool, bool, bool, bool, bool)’:
processor_support.h:43:12: note: ‘MEM[(unsigned int *)&regs + 8B]’ was declared here
   43 |     regs_t regs;
      |            ^~~~
In member function ‘ProcessorSupport::POPCNTenabled()’,
    inlined from ‘Ebwt::Ebwt<SString<char> >(SString<char>, bool, int, int, int, int, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, unsigned int, unsigned int, unsigned int, int, EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned int, RefReadInParams const&, unsigned int, int, bool, bool, bool, bool, bool)’ at bt2_idx.h:669:43:
processor_support.h:55:13: warning: ‘MEM[(unsigned int *)&regs + 8B]’ may be used uninitialized [-Wmaybe-uninitialized]
   55 |         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In member function ‘Ebwt::Ebwt<SString<char> >(SString<char>, bool, int, int, int, int, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, unsigned int, unsigned int, unsigned int, int, EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned int, RefReadInParams const&, unsigned int, int, bool, bool, bool, bool, bool)’:
processor_support.h:43:12: note: ‘MEM[(unsigned int *)&regs + 8B]’ was declared here
   43 |     regs_t regs;
      |            ^~~~
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘resize’ at ds.h:1162:14,
    inlined from ‘resize’ at ds.h:1155:7,
    inlined from ‘mkeyQSortSuf2.constprop.isra’ at multikey_qsort.h:532:34:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSuf2.constprop.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘expand’ at ds.h:1147:29,
    inlined from ‘mkeyQSortSuf2.constprop.isra’ at multikey_qsort.h:603:26:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSuf2.constprop.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘resize’ at ds.h:1162:14,
    inlined from ‘resize’ at ds.h:1155:7,
    inlined from ‘mkeyQSortSuf2.constprop.isra’ at multikey_qsort.h:532:34:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSuf2.constprop.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘expand’ at ds.h:1147:29,
    inlined from ‘mkeyQSortSuf2.constprop.isra’ at multikey_qsort.h:603:26:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSuf2.constprop.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘resize’ at ds.h:1162:14,
    inlined from ‘resize’ at ds.h:1155:7,
    inlined from ‘bucketSortSufDcU8’ at multikey_qsort.h:1042:34,
    inlined from ‘mkeyQSortSufDcU8.constprop’ at multikey_qsort.h:1162:20:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSufDcU8.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘expand’ at ds.h:1147:29,
    inlined from ‘bucketSortSufDcU8’ at multikey_qsort.h:1091:26,
    inlined from ‘mkeyQSortSufDcU8.constprop’ at multikey_qsort.h:1162:20:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSufDcU8.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘resize’ at ds.h:1162:14,
    inlined from ‘resize’ at ds.h:1155:7,
    inlined from ‘bucketSortSufDcU8’ at multikey_qsort.h:1042:34,
    inlined from ‘mkeyQSortSufDcU8.constprop’ at multikey_qsort.h:1162:20:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSufDcU8.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘expand’ at ds.h:1147:29,
    inlined from ‘bucketSortSufDcU8’ at multikey_qsort.h:1091:26,
    inlined from ‘mkeyQSortSufDcU8.constprop’ at multikey_qsort.h:1162:20:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSufDcU8.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	-I third_party \
	-o bowtie2-build-l bt2_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lpthread -lz
In file included from bt2_idx.h:60,
                 from bt2_build.cpp:28:
In member function ‘ProcessorSupport::POPCNTenabled()’,
    inlined from ‘Ebwt::Ebwt<S2bDnaString>(S2bDnaString, bool, int, int, int, int, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, unsigned long, unsigned long, unsigned long, int, EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned long, RefReadInParams const&, unsigned int, int, bool, bool, bool, bool, bool)’ at bt2_idx.h:669:43:
processor_support.h:55:13: warning: ‘MEM[(unsigned int *)&regs + 8B]’ may be used uninitialized [-Wmaybe-uninitialized]
   55 |         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In member function ‘Ebwt::Ebwt<S2bDnaString>(S2bDnaString, bool, int, int, int, int, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, unsigned long, unsigned long, unsigned long, int, EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned long, RefReadInParams const&, unsigned int, int, bool, bool, bool, bool, bool)’:
processor_support.h:43:12: note: ‘MEM[(unsigned int *)&regs + 8B]’ was declared here
   43 |     regs_t regs;
      |            ^~~~
In member function ‘ProcessorSupport::POPCNTenabled()’,
    inlined from ‘Ebwt::Ebwt<SString<char> >(SString<char>, bool, int, int, int, int, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, unsigned long, unsigned long, unsigned long, int, EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned long, RefReadInParams const&, unsigned int, int, bool, bool, bool, bool, bool)’ at bt2_idx.h:669:43:
processor_support.h:55:13: warning: ‘MEM[(unsigned int *)&regs + 8B]’ may be used uninitialized [-Wmaybe-uninitialized]
   55 |         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In member function ‘Ebwt::Ebwt<SString<char> >(SString<char>, bool, int, int, int, int, int, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, bool, bool, unsigned long, unsigned long, unsigned long, int, EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned long, RefReadInParams const&, unsigned int, int, bool, bool, bool, bool, bool)’:
processor_support.h:43:12: note: ‘MEM[(unsigned int *)&regs + 8B]’ was declared here
   43 |     regs_t regs;
      |            ^~~~
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘resize’ at ds.h:1162:14,
    inlined from ‘resize’ at ds.h:1155:7,
    inlined from ‘mkeyQSortSuf2.constprop.isra’ at multikey_qsort.h:532:34:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSuf2.constprop.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘expand’ at ds.h:1147:29,
    inlined from ‘mkeyQSortSuf2.constprop.isra’ at multikey_qsort.h:603:26:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSuf2.constprop.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘resize’ at ds.h:1162:14,
    inlined from ‘resize’ at ds.h:1155:7,
    inlined from ‘mkeyQSortSuf2.constprop.isra’ at multikey_qsort.h:532:34:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSuf2.constprop.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘expand’ at ds.h:1147:29,
    inlined from ‘mkeyQSortSuf2.constprop.isra’ at multikey_qsort.h:603:26:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSuf2.constprop.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘resize’ at ds.h:1162:14,
    inlined from ‘resize’ at ds.h:1155:7,
    inlined from ‘bucketSortSufDcU8’ at multikey_qsort.h:1042:34,
    inlined from ‘mkeyQSortSufDcU8.constprop’ at multikey_qsort.h:1162:20:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSufDcU8.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘expand’ at ds.h:1147:29,
    inlined from ‘bucketSortSufDcU8’ at multikey_qsort.h:1091:26,
    inlined from ‘mkeyQSortSufDcU8.constprop’ at multikey_qsort.h:1162:20:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSufDcU8.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘resize’ at ds.h:1162:14,
    inlined from ‘resize’ at ds.h:1155:7,
    inlined from ‘bucketSortSufDcU8’ at multikey_qsort.h:1042:34,
    inlined from ‘mkeyQSortSufDcU8.constprop’ at multikey_qsort.h:1162:20:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSufDcU8.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopy’ at ds.h:1327:28,
    inlined from ‘expand’ at ds.h:1147:29,
    inlined from ‘bucketSortSufDcU8’ at multikey_qsort.h:1091:26,
    inlined from ‘mkeyQSortSufDcU8.constprop’ at multikey_qsort.h:1162:20:
ds.h:1290:37: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
 1290 |                 EList<T, S1> *tmp = new EList<T, S1>[sz];
      |                                     ^
/usr/include/c++/14/new: In function ‘mkeyQSortSufDcU8.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
	-I third_party \
	-o bowtie2-align-s bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lpthread -lz
In file included from aligner_sw.h:75,
                 from bt2_search.cpp:54:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
bt2_search.cpp: In function ‘read_dir(char const*, int*)’:
bt2_search.cpp:4607:67: warning: pointer ‘dir_34’ may be used after ‘closedir’ [-Wuse-after-free]
 4607 |                 cerr << "read_dir: could not close directory " << dir << endl;
      |                                                                   ^~~
bt2_search.cpp:4605:20: note: call to ‘closedir’ here
 4605 |         if(closedir(dir) != 0) {
      |            ~~~~~~~~^~~~~
In file included from bt2_idx.h:60,
                 from bt2_search.cpp:41:
In member function ‘ProcessorSupport::POPCNTenabled()’,
    inlined from ‘Ebwt::Ebwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, bool, int, int, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)’ at bt2_idx.h:596:43:
processor_support.h:55:13: warning: ‘MEM[(unsigned int *)&regs + 8B]’ may be used uninitialized [-Wmaybe-uninitialized]
   55 |         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In member function ‘Ebwt::Ebwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, bool, int, int, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)’:
processor_support.h:43:12: note: ‘MEM[(unsigned int *)&regs + 8B]’ was declared here
   43 |     regs_t regs;
      |            ^~~~
In file included from /usr/include/c++/14/istream:41,
                 from /usr/include/c++/14/fstream:40,
                 from bt2_search.cpp:22:
In member function ‘std::basic_ostream<char, std::char_traits<char> >::operator<<(void const*)’,
    inlined from ‘read_dir(char const*, int*)’ at bt2_search.cpp:4607:53,
    inlined from ‘steal_threads<std::thread>(int, int, EList<int, 128>&, EList<std::thread*, 128>&)void’ at bt2_search.cpp:4623:27,
    inlined from ‘thread_monitor<std::thread>(int, int, EList<int, 128>&, EList<std::thread*, 128>&)void’ at bt2_search.cpp:4644:16,
    inlined from ‘multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4767:18:
/usr/include/c++/14/ostream:299:25: warning: pointer may be used after ‘closedir’ [-Wuse-after-free]
  299 |       { return _M_insert(__p); }
      |                ~~~~~~~~~^~~~~
In function ‘read_dir(char const*, int*)’,
    inlined from ‘steal_threads<std::thread>(int, int, EList<int, 128>&, EList<std::thread*, 128>&)void’ at bt2_search.cpp:4623:27,
    inlined from ‘thread_monitor<std::thread>(int, int, EList<int, 128>&, EList<std::thread*, 128>&)void’ at bt2_search.cpp:4644:16,
    inlined from ‘multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4767:18:
bt2_search.cpp:4605:20: note: call to ‘closedir’ here
 4605 |         if(closedir(dir) != 0) {
      |            ~~~~~~~~^~~~~
In file included from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopyExact’ at ds.h:965:7,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘expand’ at ds.h:505:29,
    inlined from ‘instantiateSeeds.isra’ at aligner_seed.cpp:560:15:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In member function ‘instantiateSeeds.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘expand’ at ds.h:505:29,
    inlined from ‘parseFasta’ at sequence_io.h:88:15:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In function ‘parseFasta’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘expand’ at ds.h:505:29,
    inlined from ‘parseFasta’ at sequence_io.h:89:14:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In function ‘parseFasta’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopyExact’ at ds.h:965:7,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘ensure’ at ds.h:467:13,
    inlined from ‘init’ at group_walk.h:1125:13,
    inlined from ‘init’ at aligner_seed2.h:2161:16,
    inlined from ‘go.isra’ at aligner_driver.cpp:317:16:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In member function ‘go.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopyExact’ at ds.h:965:7,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘ensure’ at ds.h:467:13,
    inlined from ‘advanceElement’ at group_walk.h:1179:14,
    inlined from ‘next’ at aligner_seed2.h:2203:30,
    inlined from ‘go.isra’ at aligner_driver.cpp:326:29:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In member function ‘go.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘expand’ at ds.h:505:29,
    inlined from ‘__ct ’ at pat.cpp:592:15,
    inlined from ‘patsrcFromStrings’ at pat.cpp:101:57:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In function ‘patsrcFromStrings’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘__ct ’,
    inlined from ‘driver.constprop’ at bt2_search.cpp:4902:14:
outq.h:75:81: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   75 |                                 perThreadBuf[i] = new BTString[perThreadBufSize_];
      |                                                                                 ^
/usr/include/c++/14/new: In function ‘driver.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O3 -msse2 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	-I third_party \
	-o bowtie2-align-l bt2_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lpthread -lz
In file included from aligner_sw.h:75,
                 from bt2_search.cpp:54:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
bt2_search.cpp: In function ‘read_dir(char const*, int*)’:
bt2_search.cpp:4607:67: warning: pointer ‘dir_34’ may be used after ‘closedir’ [-Wuse-after-free]
 4607 |                 cerr << "read_dir: could not close directory " << dir << endl;
      |                                                                   ^~~
bt2_search.cpp:4605:20: note: call to ‘closedir’ here
 4605 |         if(closedir(dir) != 0) {
      |            ~~~~~~~~^~~~~
In file included from bt2_idx.h:60,
                 from bt2_search.cpp:41:
In member function ‘ProcessorSupport::POPCNTenabled()’,
    inlined from ‘Ebwt::Ebwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, bool, int, int, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)’ at bt2_idx.h:596:43:
processor_support.h:55:13: warning: ‘MEM[(unsigned int *)&regs + 8B]’ may be used uninitialized [-Wmaybe-uninitialized]
   55 |         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In member function ‘Ebwt::Ebwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, bool, int, int, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)’:
processor_support.h:43:12: note: ‘MEM[(unsigned int *)&regs + 8B]’ was declared here
   43 |     regs_t regs;
      |            ^~~~
In file included from /usr/include/c++/14/istream:41,
                 from /usr/include/c++/14/fstream:40,
                 from bt2_search.cpp:22:
In member function ‘std::basic_ostream<char, std::char_traits<char> >::operator<<(void const*)’,
    inlined from ‘read_dir(char const*, int*)’ at bt2_search.cpp:4607:53,
    inlined from ‘steal_threads<std::thread>(int, int, EList<int, 128>&, EList<std::thread*, 128>&)void’ at bt2_search.cpp:4623:27,
    inlined from ‘thread_monitor<std::thread>(int, int, EList<int, 128>&, EList<std::thread*, 128>&)void’ at bt2_search.cpp:4644:16,
    inlined from ‘multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4767:18:
/usr/include/c++/14/ostream:299:25: warning: pointer may be used after ‘closedir’ [-Wuse-after-free]
  299 |       { return _M_insert(__p); }
      |                ~~~~~~~~~^~~~~
In function ‘read_dir(char const*, int*)’,
    inlined from ‘steal_threads<std::thread>(int, int, EList<int, 128>&, EList<std::thread*, 128>&)void’ at bt2_search.cpp:4623:27,
    inlined from ‘thread_monitor<std::thread>(int, int, EList<int, 128>&, EList<std::thread*, 128>&)void’ at bt2_search.cpp:4644:16,
    inlined from ‘multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4767:18:
bt2_search.cpp:4605:20: note: call to ‘closedir’ here
 4605 |         if(closedir(dir) != 0) {
      |            ~~~~~~~~^~~~~
In file included from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_sw_driver.h:81,
                 from aligner_sw_driver.cpp:47:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In file included from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor]
  191 |         NBest<T>() { nelt_ = nbest_ = n_ = 0; }
      |                 ^
aligner_sw_nuc.h:191:17: note: remove the ‘< >’
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘expand’ at ds.h:505:29,
    inlined from ‘parseFasta’ at sequence_io.h:88:15:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In function ‘parseFasta’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘expand’ at ds.h:505:29,
    inlined from ‘parseFasta’ at sequence_io.h:89:14:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In function ‘parseFasta’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘expand’ at ds.h:505:29,
    inlined from ‘__ct ’ at pat.cpp:592:15,
    inlined from ‘patsrcFromStrings’ at pat.cpp:101:57:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In function ‘patsrcFromStrings’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘__ct ’,
    inlined from ‘driver.constprop’ at bt2_search.cpp:4902:14:
outq.h:75:81: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   75 |                                 perThreadBuf[i] = new BTString[perThreadBufSize_];
      |                                                                                 ^
/usr/include/c++/14/new: In function ‘driver.constprop’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
In member function ‘alloc’,
    inlined from ‘expandCopyExact’ at ds.h:967:17,
    inlined from ‘expandCopyExact’ at ds.h:965:7,
    inlined from ‘expandCopy’ at ds.h:958:18,
    inlined from ‘expand’ at ds.h:505:29,
    inlined from ‘instantiateSeeds.isra’ at aligner_seed.cpp:560:15:
ds.h:923:26: warning: argument 1 value ‘18446744073709551615’ exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
  923 |                 T* tmp = new T[sz];
      |                          ^
/usr/include/c++/14/new: In member function ‘instantiateSeeds.isra’:
/usr/include/c++/14/new:133:26: note: in a call to allocation function ‘operator new []’ declared here
  133 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
      |                          ^
g++ -O3 -msse2 -funroll-loops -g3 \
	-DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
	-I third_party \
	-o bowtie2-inspect-s bt2_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lpthread -lz
In file included from bt2_idx.h:60,
                 from bt2_inspect.cpp:30:
In member function ‘ProcessorSupport::POPCNTenabled()’,
    inlined from ‘Ebwt::Ebwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, bool, int, int, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)’ at bt2_idx.h:596:43:
processor_support.h:55:13: warning: ‘MEM[(unsigned int *)&regs + 8B]’ may be used uninitialized [-Wmaybe-uninitialized]
   55 |         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In member function ‘Ebwt::Ebwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, bool, int, int, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)’:
processor_support.h:43:12: note: ‘MEM[(unsigned int *)&regs + 8B]’ was declared here
   43 |     regs_t regs;
      |            ^~~~
g++ -O3 -msse2 -funroll-loops -g3 \
	-DCOMPILER_OPTIONS="\"-O3 -msse2 -funroll-loops -g3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer  -std=c++11 -DPOPCNT_CAPABILITY -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \
	-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -DBOWTIE2 -DBOWTIE_INSPECT_MAIN  -DBOWTIE_64BIT_INDEX -Wall \
	-I third_party \
	-o bowtie2-inspect-l bt2_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \
	-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes  -lpthread -lz
In file included from bt2_idx.h:60,
                 from bt2_inspect.cpp:30:
In member function ‘ProcessorSupport::POPCNTenabled()’,
    inlined from ‘Ebwt::Ebwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, bool, int, int, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)’ at bt2_idx.h:596:43:
processor_support.h:55:13: warning: ‘MEM[(unsigned int *)&regs + 8B]’ may be used uninitialized [-Wmaybe-uninitialized]
   55 |         if( !( (regs.ECX & BIT(20)) && (regs.ECX & BIT(23)) ) ) return false;
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
processor_support.h: In member function ‘Ebwt::Ebwt(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int, int, bool, int, int, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool)’:
processor_support.h:43:12: note: ‘MEM[(unsigned int *)&regs + 8B]’ was declared here
   43 |     regs_t regs;
      |            ^~~~
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.PIV63a
+ umask 022
+ cd /builddir/build/BUILD/bowtie2-2.5.1-build
+ '[' /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT
++ dirname /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build
+ mkdir /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bowtie2-2.5.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT 'INSTALL=/usr/bin/install -p' PREFIX=/usr
mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin
for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \
	cp -f $file /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin ; \
done
+ mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/man/man1
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ help2man -N -s 1 -o /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/man/man1/bowtie2.1 --version-string=2.5.1 /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin/bowtie2
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ help2man -N -s 1 -o /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/man/man1/bowtie2-build.1 --version-string=2.5.1 /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin/bowtie2-build
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ help2man -N -s 1 -o /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/man/man1/bowtie2-inspect.1 --version-string=2.5.1 /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin/bowtie2-inspect
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.5.1-5.fc42 --unique-debug-suffix -2.5.1-5.fc42.x86_64 --unique-debug-src-base bowtie2-2.5.1-5.fc42.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1
find-debuginfo: starting
Extracting debug info from 6 files
DWARF-compressing 6 files
sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/bowtie2-2.5.1-5.fc42.x86_64
4934 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT
Scanned 14 directories and 138 files,
               processed 0 inodes,
               0 modified (0 replaced + 0 rewritten),
               0 unsupported format, 0 errors
Reading /builddir/build/BUILD/bowtie2-2.5.1-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.KzWWUE
+ umask 022
+ cd /builddir/build/BUILD/bowtie2-2.5.1-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bowtie2-2.5.1
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ ./bowtie2 --version
+ grep 'version 2.5.1'
/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s version 2.5.1
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ ./bowtie2-build --version
+ grep 'version 2.5.1'
/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-build-s version 2.5.1
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ ./bowtie2-inspect --version
+ grep 'version 2.5.1'
/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-inspect-s version 2.5.1
+ sed -i '/my $binary_type/ s/"release", "debug", "sanitized"/"release"/' scripts/test/simple_tests.pl
+ ASAN_OPTIONS=halt_on_error=1
+ UBSAN_OPTIONS=halt_on_error=1
+ scripts/test/simple_tests.pl --bowtie2=./bowtie2 --bowtie2-build=./bowtie2-build --compressed
\1 better written as $1 at scripts/test/simple_tests.pl line 4674.
\1 better written as $1 at scripts/test/simple_tests.pl line 4675.
FASTA-continuous 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -F 10,9 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -F 10,9 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -F 10,9 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz"
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz"
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -F 10,1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:12
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_1	0	0	2	255	10M	*	0	0	GCATCGATCA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_2	0	0	3	255	10M	*	0	0	CATCGATCAG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
Align should not fail when first seq in ref is all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
./bowtie2     --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:15
@SQ	SN:1	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	1	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Align should not fail when multiple seqs are all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
NNNNNNNNNNNNNNN
>2
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
./bowtie2     --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:15
@SQ	SN:1	LN:15
@SQ	SN:2	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	2	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Should account for stretch of Ns at beginning (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:34
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	0	18	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	ABCDEDGHIJKLMNOP	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO
Error: Read 0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Cline 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ
Error: Read 0 has more quality values than read characters.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
trim-to: trim from 5'-end (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 5:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	7	255	12M	*	0	0	GATCAGTATCTG	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: trim from 3'-end (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 3:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: trim from 3'-end (default) (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: invalid position (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 4:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

--trim-to: trim position must be either 3 or 5
Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <i>        Files with interleaved paired-end FASTQ/FASTA reads
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <bam>      Files are unaligned BAM sorted by read name.
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --tab5             query input files are TAB5 .tab5
  --tab6             query input files are TAB6 .tab6
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -F k:<int>,i:<int> query input files are continuous FASTA where reads
                     are substrings (k-mers) extracted from a FASTA file <s>
                     and aligned at offsets 1, 1+i, 1+2i ... end of reference
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
                     If the read end is not specified then it defaults to 3 (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
  For --end-to-end:
   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

  For --local:
   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

 Alignment:
  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
  -L <int>           length of seed substrings; must be >3, <32 (22)
  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --dpad <int>       include <int> extra ref chars on sides of DP table (15)
  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
                     scan for the optimal seeded alignments
  --end-to-end       entire read must align; no clipping (on)
   OR
  --local            local alignment; ends might be soft clipped (off)

 Scoring:
  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) 
  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

 Reporting:
  (default)          look for multiple alignments, report best, with MAPQ
   OR
  -k <int>           report up to <int> alns per read; MAPQ not meaningful
   OR
  -a/--all           report all alignments; very slow, MAPQ not meaningful

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

 Paired-end:
  -I/--minins <int>  minimum fragment length (0)
  -X/--maxins <int>  maximum fragment length (500)
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads
  --dovetail         concordant when mates extend past each other
  --no-contain       not concordant when one mate alignment contains other
  --no-overlap       not concordant when mates overlap at all

 BAM:
  --align-paired-reads
                     Bowtie2 will, by default, attempt to align unpaired BAM reads.
                     Use this option to align paired-end reads instead.
  --preserve-tags    Preserve tags from the original BAM record by
                     appending them to the end of the corresponding SAM output.

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>        write unpaired reads that didn't align to <path>
  --al <path>        write unpaired reads that aligned at least once to <path>
  --un-conc <path>   write pairs that didn't align concordantly to <path>
  --al-conc <path>   write pairs that aligned concordantly at least once to <path>
    (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
    --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-unal          suppress SAM records for unaligned reads
  --no-head          suppress header lines, i.e. lines starting with @
  --no-sq            suppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.
  --sam-no-qname-trunc
                     Suppress standard behavior of truncating readname at first whitespace 
                     at the expense of generating non-standard SAM.
  --xeq              Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
  --soft-clipped-unmapped-tlen
                     Exclude soft-clipped bases when reporting TLEN
  --sam-append-comment
                     Append FASTA/FASTQ comment to SAM record

 Performance:
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'bowtie's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic
                     seed rand. gen. arbitrarily instead of using read attributes
  --version          print version information and quit
  -h/--help          print this usage message
Error: Encountered internal Bowtie 2 exception (#1)
Command: /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 
trim-to: invalid count (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim-to 5:-12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

(ERR): bowtie2-align exited with value 1
--trim-to: the number bases to trim must be at least 0
Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <i>        Files with interleaved paired-end FASTQ/FASTA reads
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <bam>      Files are unaligned BAM sorted by read name.
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --tab5             query input files are TAB5 .tab5
  --tab6             query input files are TAB6 .tab6
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -F k:<int>,i:<int> query input files are continuous FASTA where reads
                     are substrings (k-mers) extracted from a FASTA file <s>
                     and aligned at offsets 1, 1+i, 1+2i ... end of reference
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
                     If the read end is not specified then it defaults to 3 (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
  For --end-to-end:
   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

  For --local:
   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

 Alignment:
  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
  -L <int>           length of seed substrings; must be >3, <32 (22)
  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --dpad <int>       include <int> extra ref chars on sides of DP table (15)
  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
                     scan for the optimal seeded alignments
  --end-to-end       entire read must align; no clipping (on)
   OR
  --local            local alignment; ends might be soft clipped (off)

 Scoring:
  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) 
  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

 Reporting:
  (default)          look for multiple alignments, report best, with MAPQ
   OR
  -k <int>           report up to <int> alns per read; MAPQ not meaningful
   OR
  -a/--all           report all alignments; very slow, MAPQ not meaningful

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

 Paired-end:
  -I/--minins <int>  minimum fragment length (0)
  -X/--maxins <int>  maximum fragment length (500)
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads
  --dovetail         concordant when mates extend past each other
  --no-contain       not concordant when one mate alignment contains other
  --no-overlap       not concordant when mates overlap at all

 BAM:
  --align-paired-reads
                     Bowtie2 will, by default, attempt to align unpaired BAM reads.
                     Use this option to align paired-end reads instead.
  --preserve-tags    Preserve tags from the original BAM record by
                     appending them to the end of the corresponding SAM output.

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>        write unpaired reads that didn't align to <path>
  --al <path>        write unpaired reads that aligned at least once to <path>
  --un-conc <path>   write pairs that didn't align concordantly to <path>
  --al-conc <path>   write pairs that aligned concordantly at least once to <path>
    (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
    --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-unal          suppress SAM records for unaligned reads
  --no-head          suppress header lines, i.e. lines starting with @
  --no-sq            suppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.
  --sam-no-qname-trunc
                     Suppress standard behavior of truncating readname at first whitespace 
                     at the expense of generating non-standard SAM.
  --xeq              Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
  --soft-clipped-unmapped-tlen
                     Exclude soft-clipped bases when reporting TLEN
  --sam-append-comment
                     Append FASTA/FASTQ comment to SAM record

 Performance:
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'bowtie's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic
                     seed rand. gen. arbitrarily instead of using read attributes
  --version          print version information and quit
  -h/--help          print this usage message
Error: Encountered internal Bowtie 2 exception (#1)
Command: /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 
(ERR): bowtie2-align exited with value 1
Cline 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Cline 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Cline 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
Cline multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII


@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Cline multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII


@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Cline paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Cline paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII"
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Cline paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Cline paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Fastq 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fastq 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fastq 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fastq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Fastq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Fastq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz"
Fastq multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fastq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fastq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Fastq paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Fastq paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Fastq paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
r0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Fasta 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	15M	*	0	0	CATCGATCAGTATCT	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fasta 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fasta 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Fasta 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Fasta 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz"
Fasta multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	9M	=	9	19	AGCATCGAT	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YS:i:0	YT:Z:CP
Fasta paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	9M	=	9	19	AGCATCGAT	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YS:i:0	YT:Z:CP
Fasta paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Fasta paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Raw 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Raw 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Raw 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz"
Raw multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Raw multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Raw paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Raw paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Raw paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Raw paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Tabbed 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Tabbed 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more quality values than read characters.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Tabbed 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Tabbed 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Tabbed 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
Tabbed multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Tabbed multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Tabbed paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Tabbed paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Tabbed paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Tabbed paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -3 7 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
r0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Qseq 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Qseq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
./bowtie2     --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Qseq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
./bowtie2     --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
Qseq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Qseq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Qseq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
./bowtie2    --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Qseq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
./bowtie2    -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
Qseq multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2     --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Qseq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Qseq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Qseq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index	99	0	1	255	10M	=	9	19	AGCATCGATC	ABCBGACBCB	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_10_10_Index	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	ABCBCAGBCBA	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	57865494859	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	163	0	1	255	10M	=	9	19	AGCATCGATC	AGGCBBGCBG	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Qseq paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz"
MachName_RunNum_Lane_Tile_12_15_Index	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	57865494859	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	163	0	1	255	10M	=	9	19	AGCATCGATC	AGGCBBGCBG	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Left-align insertion (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet  --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	23	24	2M1I40M	*	0	0	ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-8	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:42	YT:Z:UU
Left-align deletion (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2     --quiet  --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	19	40	6M1D39M	*	0	0	ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-8	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^A39	YT:Z:UU
Left-align insertion with mismatch at LHS (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet  --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	5	24	20M1D45M	*	0	0	TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:20^A0A44	YT:Z:UU
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet  --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1192
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	3	42	38M	=	1148	0	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UP
r0	129	0	1148	1	42M	=	3	0	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YT:Z:UP
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet  --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1028
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	3	42	38M	=	982	1021	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YS:i:0	YT:Z:DP
r0	129	0	982	42	42M	=	3	-1021	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YS:i:0	YT:Z:DP
MREVERSE flag is set if mate does not align (fw:1, sam:1)
References:
>0
TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet  --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:250
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	89	0	51	42	100M	=	51	0	TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:100	YT:Z:UP
r0	165	0	51	0	*	=	51	0	CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet  --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:290
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	3	1	38M	=	246	285	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YS:i:0	YT:Z:CP
r0	147	0	246	1	42M	=	3	-285	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YS:i:0	YT:Z:CP
MD:Z 1 (fw:1, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0C39	YT:Z:UU
MD:Z 1 (fw:0, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2     --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0C39	YT:Z:UU
MD:Z 2 (fw:1, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0A39	YT:Z:UU
MD:Z 2 (fw:0, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2     --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0A39	YT:Z:UU
MD:Z 3 (fw:1, sam:1)
References:
>0
CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:0	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^TA0A39	YT:Z:UU
MD:Z 3 (fw:0, sam:1)
References:
>0
CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2     --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:0	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^TA0A39	YT:Z:UU
MD:Z 4 (fw:1, sam:1)
References:
>0
CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-12	XN:i:3	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^NN0N39	YT:Z:UU
MD:Z 4 (fw:0, sam:1)
References:
>0
CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2     --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-12	XN:i:3	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^NN0N39	YT:Z:UU
Local alignment 1 (fw:1, sam:1)
References:
>0
TTGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	4M	*	0	0	TTGT	IIII	AS:i:8	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:4	YT:Z:UU
Local alignment 1 (fw:0, sam:1)
References:
>0
TTGT
./bowtie2    --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	4M	*	0	0	TTGT	IIII	AS:i:8	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:4	YT:Z:UU
Local alignment 2 (fw:1, sam:1)
References:
>0
TTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	3M1S	*	0	0	TTGT	IIII	AS:i:6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
Local alignment 2 (fw:0, sam:1)
References:
>0
TTGA
./bowtie2    --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	3M1S	*	0	0	TTGT	IIII	AS:i:6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
Local alignment 3 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	38	13M	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:26	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
r0	256	0	9	255	8M5S	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 3 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	38	13M	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:26	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
r0	272	0	9	255	8M5S	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 4 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	37	12M	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:24	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
r0	256	0	9	255	8M4S	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 4 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	37	12M	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:24	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
r0	272	0	9	255	8M4S	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Alignment order -k (fw:1, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	256	0	22	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	256	0	46	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	256	0	71	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -k (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2    --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	272	0	22	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	272	0	46	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	272	0	71	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -a (fw:1, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2    --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	256	0	22	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	256	0	46	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	256	0	71	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -a (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2    --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	272	0	22	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	272	0	46	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	272	0	71	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Mate reporting order, -a (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	99	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	147	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	255	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	169	255	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	255	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	68	255	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	104	255	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	255	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	205	255	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	255	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	255	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	255	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	83	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	163	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	255	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	205	255	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	169	255	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	104	255	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	68	255	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	3	255	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	255	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	3	255	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	255	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	104	255	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	99	0	307	255	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
r2	147	0	379	255	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
Mate reporting order, -a (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2     --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	83	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	163	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	255	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	205	255	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	169	255	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	104	255	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	68	255	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	3	255	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	255	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	3	255	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	255	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	104	255	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	99	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	147	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	255	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	169	255	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	255	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	68	255	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	104	255	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	255	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	205	255	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	255	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	255	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	255	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	83	0	379	255	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
r2	163	0	307	255	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
Mate reporting order, -M 1 (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2     --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	99	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	147	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	83	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	163	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	99	0	307	42	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
r2	147	0	379	42	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
Mate reporting order, -M 1 (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2     --fr --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	83	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	163	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	99	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	147	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	83	0	379	42	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
r2	163	0	307	42	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
Non-overlapping; no args (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-dovetail --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-dovetail --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-overlap (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Overlapping; no args (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2     --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-dovetail --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; --no-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-contain (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-contain --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; --no-contain (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-contain --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-overlap --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
r0	129	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:DP
Overlapping; --no-overlap (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2    --no-overlap --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:DP
r0	177	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
Scoring params 1 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:105
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	42	88M	*	0	0	GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:88	YT:Z:UU
Scoring params 1 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG
./bowtie2     --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:105
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	42	88M	*	0	0	GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:88	YT:Z:UU
Scoring params 2 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-38	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 2 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-38	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 3 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-31	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 3 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-31	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 4 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-30	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 4 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-30	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 5 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-40	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 5 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-40	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 6 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-41	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 6 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2    --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-41	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Q XS:i 1a (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-5	XS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-5	XS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,3 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,3 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,6 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,6 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,3 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,3 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,6 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,6 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-4	XS:i:-4	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-4	XS:i:-4	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
(fw:1, sam:1)
References:
>0
CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:68
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	73	0	2	255	27M	=	2	0	ATCGACTGAGACTCGTACGACAATTAC	IIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:27	YT:Z:UP
r0	133	0	2	0	*	=	2	0	TAGGTTTCGCGCGAAACGCTGGTGAT	IIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
(fw:0, sam:1)
References:
>0
CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT
./bowtie2     --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:68
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	137	0	2	255	27M	=	2	0	ATCGACTGAGACTCGTACGACAATTAC	IIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:27	YT:Z:UP
r0	69	0	2	0	*	=	2	0	TAGGTTTCGCGCGAAACGCTGGTGAT	IIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:528
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	217	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT
./bowtie2    --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:528
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	89	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 1 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
XS:i 1 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
XS:i 2 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-5 --quiet  --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGT	IIIIIIII	YT:Z:UU
XS:i 2 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-5 --quiet  --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACGAACAA	IIIIIIII	YT:Z:UU
XS:i 3a (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3a (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3b (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3b (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3c (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4a (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4b (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4b (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2    --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5a (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2    --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5b (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2    --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5b (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2    --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
BWA-SW-like 1 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --bwa-sw-like --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:56	YT:Z:UU
BWA-SW-like 1 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:56	YT:Z:UU
BWA-SW-like 2 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like -L 18 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:48	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:26A0A28	YT:Z:UU
BWA-SW-like 2 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like -L 18 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:48	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:26A0A28	YT:Z:UU
BWA-SW-like 3 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	26M3D27M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:42	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:26^AAC27	YT:Z:UU
BWA-SW-like 3 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2    --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	26M3D27M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:42	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:26^AAC27	YT:Z:UU
SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	147	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	131	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --rf --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	163	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 1 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	147	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 2 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --rf --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	163	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 3 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	131	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	73	0	4	255	24M	=	4	0	CTATCTACGCTTCGGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:24	YT:Z:UP
r0	133	0	4	0	*	=	4	0	GATTGTCTTTTCCCGGAAAAATCGT	IIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
SAM paired-end where neither mate aligns (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CTATATACGAAAAAGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	GATTGTCTTTTCCCGGAAAAATCGT	IIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
SAM paired-end where both mates align, but discordantly (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2     --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:24	YS:i:0	YT:Z:DP
r0	129	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
matchesRef regression 4 (fw:1, sam:1)
References:
>0
CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC
>1
GCTCGGAATTCGTGCTCCGNCCCGTACGGTT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@SQ	SN:1	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
matchesRef regression 4 (fw:0, sam:1)
References:
>0
CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC
>1
GCTCGGAATTCGTGCTCCGNCCCGTACGGTT
./bowtie2    --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@SQ	SN:1	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
matchesRef regression 3 (fw:1, sam:1)
References:
>0
GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	10	255	38M	*	0	0	CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UU
matchesRef regression 3 (fw:0, sam:1)
References:
>0
GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC
./bowtie2    --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	10	255	38M	*	0	0	CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UU
matchesRef regression 2 (fw:1, sam:1)
References:
>0
GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG
>1
CCTTGTTNTTAATGCTGCCTGGTTTNG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@SQ	SN:1	LN:27
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
matchesRef regression 2 (fw:0, sam:1)
References:
>0
GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG
>1
CCTTGTTNTTAATGCTGCCTGGTTTNG
./bowtie2    --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@SQ	SN:1	LN:27
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	1	255	29S23M	=	1	-68	CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-78	XN:i:7	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:-128	YT:Z:CP
r0	163	0	1	255	45S15M	=	1	68	CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-128	XN:i:9	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:14T0	YS:i:-78	YT:Z:CP
matchesRef regression 1 (fw:1, sam:1)
References:
>0
AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:61
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	12	255	50M10S	*	0	0	AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:9	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
matchesRef regression 1 (fw:0, sam:1)
References:
>0
AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC
./bowtie2    --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:61
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	12	255	50M10S	*	0	0	AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:9	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
Discordant with different chromosomes (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCC
>1
CCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:23
@SQ	SN:1	LN:28
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	65	0	4	255	10M	1	8	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	1	8	255	10M	0	4	0	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	65	0	4	255	10M	1	7	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	129	1	7	255	10M	0	4	0	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Discordant with different chromosomes (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCC
>1
CCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2    -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:23
@SQ	SN:1	LN:28
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	113	1	8	255	10M	0	4	0	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	1	8	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	113	1	7	255	10M	0	4	0	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	177	0	4	255	10M	1	7	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r1	99	0	1	255	10M	=	10	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	147	0	10	255	10M	=	1	-19	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r1	83	0	10	255	10M	=	1	-19	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	10	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 2 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r1	0	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r1	16	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --trim3 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	4	255	9M	*	0	0	ATCGATCAG	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --trim3 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	6	255	9M	*	0	0	CGATCAGTA	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --trim5 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	4	255	9M	*	0	0	ATCGATCAG	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2    -s 1 --trim5 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	6	255	9M	*	0	0	CGATCAGTA	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:1, sam:1)
References:
>0
TGC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:3
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	1S3M	*	0	0	ATGC	IIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
(fw:0, sam:1)
References:
>0
TGC
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:3
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	1S3M	*	0	0	ATGC	IIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
r2	0	0	1	255	1S6M	*	0	0	ATTGTTC	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
r2	16	0	1	255	1S6M	*	0	0	ATTGTTC	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r2	4	*	0	0	*	*	0	0	GTTCGTA	IIIIIII	YT:Z:UU
r3	4	*	0	0	*	*	0	0	ATTGTTC	IIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r2	4	*	0	0	*	*	0	0	TACGAAC	IIIIIII	YT:Z:UU
r3	4	*	0	0	*	*	0	0	GAACAAT	IIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -X 1000 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --local --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --local --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --fr --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	255	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	724	255	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	255	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	790	255	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	255	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	961	255	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	255	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	487	255	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	724	255	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	255	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	790	255	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	255	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	961	255	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	255	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	487	255	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	255	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	255	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	724	255	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	255	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	790	255	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	255	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	961	255	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	255	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	487	255	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2    -X 1000 --local --fr --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	553	1	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	724	255	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	255	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	790	255	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	255	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	961	255	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	255	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	487	255	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	255	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -M 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -M 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -M 1 --local -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -M 1 --local -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	1	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2     --fr --quiet -k 1 -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	42	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	42	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	42	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	42	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --local --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	44	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	44	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2    -X 150 --local --fr --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	44	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	44	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -X 150 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:2607
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	1435	1	33M	=	1501	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	1501	1	28M	=	1435	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA
./bowtie2    -X 150 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:2607
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	790	1	28M	=	724	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	724	1	33M	=	790	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --local -X 150 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1906
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC
./bowtie2    --local -X 150 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1906
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	42	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2     --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	42	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2    --local --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	44	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2    --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	44	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2     --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2     --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2    --local --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2    --local --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -M 2 --local --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	49	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -k 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	49	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -X 150 --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	304	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	134	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	177	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	219	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2     --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	134	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	49	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	219	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	304	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	134	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	177	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	49	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	219	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2    --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	134	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	49	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	219	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
r0	256	0	1	255	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
r0	272	0	1	255	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCAT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATGAACAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2    --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
Gap penalties 1 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	6M1D6M	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	AS:i:-39	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^G6	YT:Z:UU
Gap penalties 1 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	6M1D6M	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	AS:i:-39	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^G6	YT:Z:UU
Gap penalties 2 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	YT:Z:UU
Gap penalties 2 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAAGAACAA	IIIIIIIIIIII	YT:Z:UU
Gap penalties 3 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
Gap penalties 3 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
Gap penalties 4 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 4 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAATCGAACAA	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 5 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 5 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAATCGAACAA	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 6 (fw:1, sam:1)
References:
>0
ATTGTTCGTTTGTTCGTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:18
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	6M1D5M1I6M	*	0	0	ATTGTTGTTTGATTCGTA	IIIIIIIIIIIIIIIIII	AS:i:-57	XN:i:0	XM:i:0	XO:i:2	XG:i:2	NM:i:2	MD:Z:6^C11	YT:Z:UU
Gap penalties 6 (fw:0, sam:1)
References:
>0
ATTGTTCGTTTGTTCGTA
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:18
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	6M1D5M1I6M	*	0	0	ATTGTTGTTTGATTCGTA	IIIIIIIIIIIIIIIIII	AS:i:-57	XN:i:0	XM:i:0	XO:i:2	XG:i:2	NM:i:2	MD:Z:6^C11	YT:Z:UU
Gap penalties 7 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTGTTTGATTCGT	IIIIIIIIIIIIIIII	YT:Z:UU
Gap penalties 7 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACGAATCAAACAACAA	IIIIIIIIIIIIIIII	YT:Z:UU
N filtering 1 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
N filtering 1 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
N filtering 2 (fw:1, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 2 (fw:0, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 3 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 3 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 4 (fw:1, sam:1)
References:
>0
GAGACTTTNTACGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 4 (fw:0, sam:1)
References:
>0
GAGACTTTNTACGCATCGAACTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 5 (fw:1, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:2N10	YT:Z:UU
N filtering 5 (fw:0, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:2N10	YT:Z:UU
N filtering 6 (fw:1, sam:1)
References:
>0
GAGACTTTNTACGCATCGAANTATCGCTCTA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 6 (fw:0, sam:1)
References:
>0
GAGACTTTNTACGCATCGAANTATCGCTCTA
./bowtie2    --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	9M1I4M	*	0	0	TTTTGTTCGATTTG	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	9M1I4M	*	0	0	TTTTGTTCGATTTG	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCA
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	2M	*	0	0	CA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCA
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	2M	*	0	0	CA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (1) (fw:1, sam:1)
References:
>0
ACNCA
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	2M	*	0	0	AC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (1) (fw:0, sam:1)
References:
>0
ACNCA
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	2M	*	0	0	AC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (2) (fw:1, sam:1)
References:
>0
ACNCANNNNNNNNCGNNNNNNNNCG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:25
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (2) (fw:0, sam:1)
References:
>0
ACNCANNNNNNNNCGNNNNNNNNCG
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:25
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	14	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTYGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	1	255	8M	*	0	0	TTGTTGGT	IIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:5N2	YT:Z:UU
r1	0	0	1	255	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:5N2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATAACCTTCG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:10
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	4M2D4M	*	0	0	ATAATTCG	IIIIIIII	AS:i:-15	XN:i:0	XM:i:0	XO:i:1	XG:i:2	NM:i:2	MD:Z:4^CC4	YT:Z:UU
(fw:0, sam:1)
References:
>0
ATAACCTTCG
./bowtie2     --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:10
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	4M2D4M	*	0	0	ATAATTCG	IIIIIIII	AS:i:-15	XN:i:0	XM:i:0	XO:i:1	XG:i:2	NM:i:2	MD:Z:4^CC4	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATATGCCCCATGCCCCCCTCCG
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:22
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	9M3D10M	*	0	0	ATATGCCCCCCCCCCTCCG	IIIIIIIIIIIIIIIIIII	AS:i:-20	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:9^ATG10	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATATGCCCCATGCCCCCCTCCG
./bowtie2     --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:22
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	9M3D10M	*	0	0	ATATGCCCCCCCCCCTCCG	IIIIIIIIIIIIIIIIIII	AS:i:-20	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:9^ATG10	YT:Z:UU
Simple paired-end 13 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 35 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	65	0	4	255	10M	=	30	36	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	129	0	30	255	10M	=	4	-36	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r2	67	0	4	255	10M	=	29	35	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r2	131	0	29	255	10M	=	4	-35	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	67	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	131	0	28	255	10M	=	4	-34	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r4	65	0	5	255	10M	=	31	36	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r4	129	0	31	255	10M	=	5	-36	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r5	67	0	5	255	10M	=	30	35	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r5	131	0	30	255	10M	=	5	-35	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	67	0	5	255	10M	=	29	34	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	131	0	29	255	10M	=	5	-34	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	67	0	5	255	10M	=	28	33	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	131	0	28	255	10M	=	5	-33	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 13 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2    -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz"
r0	113	0	31	255	10M	=	4	-37	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	113	0	30	255	10M	=	4	-36	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	177	0	4	255	10M	=	30	36	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r2	115	0	29	255	10M	=	4	-35	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r2	179	0	4	255	10M	=	29	35	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	115	0	28	255	10M	=	4	-34	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	179	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r4	113	0	31	255	10M	=	5	-36	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r4	177	0	5	255	10M	=	31	36	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r5	115	0	30	255	10M	=	5	-35	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r5	179	0	5	255	10M	=	30	35	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	115	0	29	255	10M	=	5	-34	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	179	0	5	255	10M	=	29	34	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	115	0	28	255	10M	=	5	-33	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	179	0	5	255	10M	=	28	33	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 12 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	GGCCCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	67	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	131	0	28	255	10M	=	4	-34	CCGGGCCCGC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 12 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC
./bowtie2    -I 0 -X 36 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	113	0	31	255	10M	=	4	-37	GGCCCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	115	0	28	255	10M	=	4	-34	CCGGGCCCGC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	179	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 11 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 11 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2    -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	31	255	10M	=	4	-37	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 10 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 28 -X 80 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:41
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	10M	=	21	27	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	21	255	10M	=	4	-27	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 10 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2    -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:41
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	21	255	10M	=	4	-27	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	21	27	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 9 (fw:1, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	20	1	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	60	1	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 9 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2    -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	60	1	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	163	0	20	1	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 8 (fw:1, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	20	1	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	60	1	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	355	0	4	255	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	403	0	60	255	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	355	0	38	255	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	403	0	60	255	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 8 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2    -I 0 -X 80 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	60	1	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	163	0	20	1	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	339	0	60	255	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	419	0	4	255	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	339	0	60	255	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	419	0	38	255	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 2; no --no-mixed (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	153	0	4	255	10M	=	4	0	ATATATATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UP
r0	101	0	4	0	*	=	4	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
Simple paired-end 2; --no-mixed (fw:1, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	ATATATATAT	IIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
Simple paired-end 2; --no-mixed (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC
./bowtie2    -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	ATATATATAT	IIIIIIIIII	YT:Z:UP
Simple paired-end 1 (fw:1, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    -I 0 -X 50 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	10M	=	36	42	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	131	0	36	255	10M	=	4	-42	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 1 (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC
./bowtie2    -I 0 -X 50 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	36	255	10M	=	4	-42	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	179	0	4	255	10M	=	36	42	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	4	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	44	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	42	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2     --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	14	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	26	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	17	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	40	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2    --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build  --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2     --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2     --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy SEED=0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	256	0	1	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	256	0	5	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-3	XS:i:-2	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:1C0G2T2	YT:Z:UU
r0	256	0	4	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2C0G1T0T0G0	YT:Z:UU
r0	256	0	8	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2T0G1T0C0G0	YT:Z:UU
r0	256	0	6	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:0C0G0T2G0T1	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2    --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	272	0	9	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	272	0	5	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-3	XS:i:-2	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:1C0G2T2	YT:Z:UU
r0	272	0	6	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:0C0G0T2G0T1	YT:Z:UU
r0	272	0	4	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2C0G1T0T0G0	YT:Z:UU
r0	272	0	8	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2T0G1T0C0G0	YT:Z:UU
FASTA-continuous 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -F 10,9 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -F 10,9 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq2_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz"
seq1_9	0	0	10	255	10M	*	0	0	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz"
seq2_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
FASTA-continuous 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -F 10,1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp  .simple_tests.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:12
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz"
seq1_0	0	0	1	255	10M	*	0	0	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_1	0	0	2	255	10M	*	0	0	GCATCGATCA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
seq1_2	0	0	3	255	10M	*	0	0	CATCGATCAG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UU
Align should not fail when first seq in ref is all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
./bowtie2   --large-index  --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:15
@SQ	SN:1	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	1	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Align should not fail when multiple seqs are all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
NNNNNNNNNNNNNNN
>2
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
./bowtie2   --large-index  --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:15
@SQ	SN:1	LN:15
@SQ	SN:2	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	2	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Should account for stretch of Ns at beginning (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:34
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	0	18	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	ABCDEDGHIJKLMNOP	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO
Error: Read 0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Cline 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ
Error: Read 0 has more quality values than read characters.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
trim-to: trim from 5'-end (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim-to 5:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	7	255	12M	*	0	0	GATCAGTATCTG	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: trim from 3'-end (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim-to 3:12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: trim from 3'-end (default) (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim-to 12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
trim-to: invalid position (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim-to 4:12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

--trim-to: trim position must be either 3 or 5
Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2l).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <i>        Files with interleaved paired-end FASTQ/FASTA reads
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <bam>      Files are unaligned BAM sorted by read name.
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --tab5             query input files are TAB5 .tab5
  --tab6             query input files are TAB6 .tab6
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -F k:<int>,i:<int> query input files are continuous FASTA where reads
                     are substrings (k-mers) extracted from a FASTA file <s>
                     and aligned at offsets 1, 1+i, 1+2i ... end of reference
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
                     If the read end is not specified then it defaults to 3 (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
  For --end-to-end:
   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

  For --local:
   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

 Alignment:
  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
  -L <int>           length of seed substrings; must be >3, <32 (22)
  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --dpad <int>       include <int> extra ref chars on sides of DP table (15)
  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
                     scan for the optimal seeded alignments
  --end-to-end       entire read must align; no clipping (on)
   OR
  --local            local alignment; ends might be soft clipped (off)

 Scoring:
  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) 
  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

 Reporting:
  (default)          look for multiple alignments, report best, with MAPQ
   OR
  -k <int>           report up to <int> alns per read; MAPQ not meaningful
   OR
  -a/--all           report all alignments; very slow, MAPQ not meaningful

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

 Paired-end:
  -I/--minins <int>  minimum fragment length (0)
  -X/--maxins <int>  maximum fragment length (500)
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads
  --dovetail         concordant when mates extend past each other
  --no-contain       not concordant when one mate alignment contains other
  --no-overlap       not concordant when mates overlap at all

 BAM:
  --align-paired-reads
                     Bowtie2 will, by default, attempt to align unpaired BAM reads.
                     Use this option to align paired-end reads instead.
  --preserve-tags    Preserve tags from the original BAM record by
                     appending them to the end of the corresponding SAM output.

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>        write unpaired reads that didn't align to <path>
  --al <path>        write unpaired reads that aligned at least once to <path>
  --un-conc <path>   write pairs that didn't align concordantly to <path>
  --al-conc <path>   write pairs that aligned concordantly at least once to <path>
    (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
    --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-unal          suppress SAM records for unaligned reads
  --no-head          suppress header lines, i.e. lines starting with @
  --no-sq            suppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.
  --sam-no-qname-trunc
                     Suppress standard behavior of truncating readname at first whitespace 
                     at the expense of generating non-standard SAM.
  --xeq              Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
  --soft-clipped-unmapped-tlen
                     Exclude soft-clipped bases when reporting TLEN
  --sam-append-comment
                     Append FASTA/FASTQ comment to SAM record

 Performance:
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'bowtie's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic
                     seed rand. gen. arbitrarily instead of using read attributes
  --version          print version information and quit
  -h/--help          print this usage message
Error: Encountered internal Bowtie 2 exception (#1)
Command: /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 
(ERR): bowtie2-align exited with value 1
trim-to: invalid count (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

--trim-to: the number bases to trim must be at least 0
Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage: 
  bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]

  <bt2-idx>  Index filename prefix (minus trailing .X.bt2l).
             NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
  <m1>       Files with #1 mates, paired with files in <m2>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <m2>       Files with #2 mates, paired with files in <m1>.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <r>        Files with unpaired reads.
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <i>        Files with interleaved paired-end FASTQ/FASTA reads
             Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
  <bam>      Files are unaligned BAM sorted by read name.
  <sam>      File for SAM output (default: stdout)

  <m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
  specified many times.  E.g. '-U file1.fq,file2.fq -U file3.fq'.

Options (defaults in parentheses):

 Input:
  -q                 query input files are FASTQ .fq/.fastq (default)
  --tab5             query input files are TAB5 .tab5
  --tab6             query input files are TAB6 .tab6
  --qseq             query input files are in Illumina's qseq format
  -f                 query input files are (multi-)FASTA .fa/.mfa
  -r                 query input files are raw one-sequence-per-line
  -F k:<int>,i:<int> query input files are continuous FASTA where reads
                     are substrings (k-mers) extracted from a FASTA file <s>
                     and aligned at offsets 1, 1+i, 1+2i ... end of reference
  -c                 <m1>, <m2>, <r> are sequences themselves, not files
  -s/--skip <int>    skip the first <int> reads/pairs in the input (none)
  -u/--upto <int>    stop after first <int> reads/pairs (no limit)
  -5/--trim5 <int>   trim <int> bases from 5'/left end of reads (0)
  -3/--trim3 <int>   trim <int> bases from 3'/right end of reads (0)
  --trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
                     If the read end is not specified then it defaults to 3 (0)
  --phred33          qualities are Phred+33 (default)
  --phred64          qualities are Phred+64
  --int-quals        qualities encoded as space-delimited integers

 Presets:                 Same as:
  For --end-to-end:
   --very-fast            -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
   --fast                 -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
   --sensitive            -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
   --very-sensitive       -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

  For --local:
   --very-fast-local      -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
   --fast-local           -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
   --sensitive-local      -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
   --very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

 Alignment:
  -N <int>           max # mismatches in seed alignment; can be 0 or 1 (0)
  -L <int>           length of seed substrings; must be >3, <32 (22)
  -i <func>          interval between seed substrings w/r/t read len (S,1,1.15)
  --n-ceil <func>    func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
  --dpad <int>       include <int> extra ref chars on sides of DP table (15)
  --gbar <int>       disallow gaps within <int> nucs of read extremes (4)
  --ignore-quals     treat all quality values as 30 on Phred scale (off)
  --nofw             do not align forward (original) version of read (off)
  --norc             do not align reverse-complement version of read (off)
  --no-1mm-upfront   do not allow 1 mismatch alignments before attempting to
                     scan for the optimal seeded alignments
  --end-to-end       entire read must align; no clipping (on)
   OR
  --local            local alignment; ends might be soft clipped (off)

 Scoring:
  --ma <int>         match bonus (0 for --end-to-end, 2 for --local) 
  --mp <int>         max penalty for mismatch; lower qual = lower penalty (6)
  --np <int>         penalty for non-A/C/G/Ts in read/ref (1)
  --rdg <int>,<int>  read gap open, extend penalties (5,3)
  --rfg <int>,<int>  reference gap open, extend penalties (5,3)
  --score-min <func> min acceptable alignment score w/r/t read length
                     (G,20,8 for local, L,-0.6,-0.6 for end-to-end)

 Reporting:
  (default)          look for multiple alignments, report best, with MAPQ
   OR
  -k <int>           report up to <int> alns per read; MAPQ not meaningful
   OR
  -a/--all           report all alignments; very slow, MAPQ not meaningful

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

 Paired-end:
  -I/--minins <int>  minimum fragment length (0)
  -X/--maxins <int>  maximum fragment length (500)
  --fr/--rf/--ff     -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
  --no-mixed         suppress unpaired alignments for paired reads
  --no-discordant    suppress discordant alignments for paired reads
  --dovetail         concordant when mates extend past each other
  --no-contain       not concordant when one mate alignment contains other
  --no-overlap       not concordant when mates overlap at all

 BAM:
  --align-paired-reads
                     Bowtie2 will, by default, attempt to align unpaired BAM reads.
                     Use this option to align paired-end reads instead.
  --preserve-tags    Preserve tags from the original BAM record by
                     appending them to the end of the corresponding SAM output.

 Output:
  -t/--time          print wall-clock time taken by search phases
  --un <path>        write unpaired reads that didn't align to <path>
  --al <path>        write unpaired reads that aligned at least once to <path>
  --un-conc <path>   write pairs that didn't align concordantly to <path>
  --al-conc <path>   write pairs that aligned concordantly at least once to <path>
    (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
    --un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
  --quiet            print nothing to stderr except serious errors
  --met-file <path>  send metrics to file at <path> (off)
  --met-stderr       send metrics to stderr (off)
  --met <int>        report internal counters & metrics every <int> secs (1)
  --no-unal          suppress SAM records for unaligned reads
  --no-head          suppress header lines, i.e. lines starting with @
  --no-sq            suppress @SQ header lines
  --rg-id <text>     set read group id, reflected in @RG line and RG:Z: opt field
  --rg <text>        add <text> ("lab:value") to @RG line of SAM header.
                     Note: @RG line only printed when --rg-id is set.
  --omit-sec-seq     put '*' in SEQ and QUAL fields for secondary alignments.
  --sam-no-qname-trunc
                     Suppress standard behavior of truncating readname at first whitespace 
                     at the expense of generating non-standard SAM.
  --xeq              Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
  --soft-clipped-unmapped-tlen
                     Exclude soft-clipped bases when reporting TLEN
  --sam-append-comment
                     Append FASTA/FASTQ comment to SAM record

 Performance:
  -p/--threads <int> number of alignment threads to launch (1)
  --reorder          force SAM output order to match order of input reads
  --mm               use memory-mapped I/O for index; many 'bowtie's can share

 Other:
  --qc-filter        filter out reads that are bad according to QSEQ filter
  --seed <int>       seed for random number generator (0)
  --non-deterministic
                     seed rand. gen. arbitrarily instead of using read attributes
  --version          print version information and quit
  -h/--help          print this usage message
Error: Encountered internal Bowtie 2 exception (#1)
Command: /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII 
Cline 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII

(ERR): bowtie2-align exited with value 1
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Cline 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Cline 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
Cline multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII


@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Cline multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII


@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Cline multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG

@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Cline paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Cline paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII"
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Cline paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Cline paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Fastq 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fastq 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
Fastq 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
./bowtie2   --large-index  --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: reads file does not look like a FASTQ file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fastq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Fastq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim5 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Fastq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz"
Fastq multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fastq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fastq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fastq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Fastq paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Fastq paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Fastq paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
r0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Fasta 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	15M	*	0	0	CATCGATCAGTATCT	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fasta 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fasta 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Fasta 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Fasta 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz"
Fasta multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Fasta multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta multiline 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Fasta paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	9M	=	9	19	AGCATCGAT	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YS:i:0	YT:Z:CP
Fasta paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	9M	=	9	19	AGCATCGAT	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YS:i:0	YT:Z:CP
Fasta paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Fasta paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Raw 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Raw 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Raw 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz"
Raw multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Raw multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Raw multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Raw paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Raw paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Raw paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Raw paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Tabbed 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Tabbed 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more quality values than read characters.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Tabbed 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Tabbed 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim5 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Tabbed 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
Tabbed multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Tabbed multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Tabbed multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r1	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Tabbed paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Tabbed paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r1	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Tabbed paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	99	0	1	255	10M	=	9	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
Tabbed paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0	137	0	7	255	6M	=	7	0	GATCAA	IIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UP
r0	69	0	7	0	*	=	7	0	*	*	YT:Z:UP	YF:Z:LN
Qseq 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
Qseq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
Qseq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
Qseq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Qseq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	0	0	3	255	12M	*	0	0	CATCGATCAGTA	IIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
Qseq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0	4	*	0	0	*	*	0	0	*	*	YT:Z:UU	YF:Z:LN
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052.
Qseq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
Qseq multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index  --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Qseq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
Qseq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0	0	0	3	255	16M	*	0	0	CATCGATCAGTATCTG	IIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0	0	0	4	255	15M	*	0	0	ATCGATCAGTATCTG	IIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:15	YT:Z:UU
Qseq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index	99	0	1	255	10M	=	9	19	AGCATCGATC	ABCBGACBCB	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_10_10_Index	147	0	9	255	11M	=	1	-19	TCAAAAACTGA	ABCBCAGBCBA	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	57865494859	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	163	0	1	255	10M	=	9	19	AGCATCGATC	AGGCBBGCBG	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Qseq paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz"
MachName_RunNum_Lane_Tile_12_15_Index	83	0	9	255	11M	=	1	-19	TCAAAAACTGA	57865494859	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YS:i:0	YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index	163	0	1	255	10M	=	9	19	AGCATCGATC	AGGCBBGCBG	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Left-align insertion (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet  --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	23	24	2M1I40M	*	0	0	ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-8	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:42	YT:Z:UU
Left-align deletion (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2   --large-index  --quiet  --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	19	40	6M1D39M	*	0	0	ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-8	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^A39	YT:Z:UU
Left-align insertion with mismatch at LHS (fw:1, sam:1)
References:
>0
GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet  --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:73
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	5	24	20M1D45M	*	0	0	TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:20^A0A44	YT:Z:UU
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --fr --quiet  --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1192
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	3	42	38M	=	1065	0	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UP
r0	129	0	1065	1	42M	=	3	0	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YT:Z:UP
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --fr --quiet  --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1028
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	3	42	38M	=	982	1021	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YS:i:0	YT:Z:DP
r0	129	0	982	42	42M	=	3	-1021	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YS:i:0	YT:Z:DP
MREVERSE flag is set if mate does not align (fw:1, sam:1)
References:
>0
TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --fr --quiet  --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:250
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	89	0	51	42	100M	=	51	0	TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:100	YT:Z:UP
r0	165	0	51	0	*	=	51	0	CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --fr --quiet  --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:290
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	3	1	38M	=	246	285	GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YS:i:0	YT:Z:CP
r0	147	0	246	1	42M	=	3	-285	ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:42	YS:i:0	YT:Z:CP
MD:Z 1 (fw:1, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0C39	YT:Z:UU
MD:Z 1 (fw:0, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2   --large-index  --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0C39	YT:Z:UU
MD:Z 2 (fw:1, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0A39	YT:Z:UU
MD:Z 2 (fw:0, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2   --large-index  --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:54
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M1D40M	*	0	0	CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-14	XN:i:0	XM:i:1	XO:i:1	XG:i:1	NM:i:2	MD:Z:13^A0A39	YT:Z:UU
MD:Z 3 (fw:1, sam:1)
References:
>0
CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:0	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^TA0A39	YT:Z:UU
MD:Z 3 (fw:0, sam:1)
References:
>0
CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2   --large-index  --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:0	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^TA0A39	YT:Z:UU
MD:Z 4 (fw:1, sam:1)
References:
>0
CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-12	XN:i:3	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^NN0N39	YT:Z:UU
MD:Z 4 (fw:0, sam:1)
References:
>0
CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2   --large-index  --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:55
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	13M2D40M	*	0	0	CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-12	XN:i:3	XM:i:1	XO:i:1	XG:i:2	NM:i:3	MD:Z:13^NN0N39	YT:Z:UU
Local alignment 1 (fw:1, sam:1)
References:
>0
TTGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	4M	*	0	0	TTGT	IIII	AS:i:8	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:4	YT:Z:UU
Local alignment 1 (fw:0, sam:1)
References:
>0
TTGT
./bowtie2   --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	4M	*	0	0	TTGT	IIII	AS:i:8	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:4	YT:Z:UU
Local alignment 2 (fw:1, sam:1)
References:
>0
TTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	3M1S	*	0	0	TTGT	IIII	AS:i:6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
Local alignment 2 (fw:0, sam:1)
References:
>0
TTGA
./bowtie2   --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:4
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	3M1S	*	0	0	TTGT	IIII	AS:i:6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
Local alignment 3 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	38	13M	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:26	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
r0	256	0	9	255	8M5S	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 3 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	38	13M	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:26	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
r0	272	0	9	255	8M5S	*	0	0	TTGTTCGTTTGTT	IIIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 4 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	37	12M	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:24	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
r0	256	0	9	255	8M4S	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Local alignment 4 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	37	12M	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:24	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:12	YT:Z:UU
r0	272	0	9	255	8M4S	*	0	0	TTGTTCGTTTGT	IIIIIIIIIIII	AS:i:16	XS:i:16	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
Alignment order -k (fw:1, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	256	0	22	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	256	0	46	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	256	0	71	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -k (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2   --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	272	0	22	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	272	0	46	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	272	0	71	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -a (fw:1, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2   --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	256	0	22	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	256	0	46	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	256	0	71	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Alignment order -a (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2   --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:86
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	31	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:16	YT:Z:UU
r0	272	0	22	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:15T0	YT:Z:UU
r0	272	0	46	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-12	XS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14T0T0	YT:Z:UU
r0	272	0	71	255	16M	*	0	0	GCGCATGCACATATCA	GOAIYEFGFIWDSFIU	AS:i:-22	XS:i:-6	XN:i:0	XM:i:4	XO:i:0	XG:i:0	NM:i:4	MD:Z:7G0T0G0T5	YT:Z:UU
Mate reporting order, -a (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	99	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	147	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	255	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	255	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	205	255	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	255	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	255	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	68	255	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	104	255	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	270	255	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	355	0	3	255	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	403	0	169	255	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	83	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	163	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	255	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	104	255	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	169	255	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	104	255	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	255	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	205	255	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	68	255	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	3	255	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	339	0	270	255	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	419	0	3	255	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	99	0	307	255	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
r2	147	0	379	255	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
Mate reporting order, -a (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2   --large-index  --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	83	0	169	1	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	163	0	3	1	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	255	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	104	255	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	169	255	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	104	255	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	255	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	205	255	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	68	255	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	3	255	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	339	0	270	255	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	419	0	3	255	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	99	0	104	1	19M	=	169	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	147	0	169	1	19M	=	104	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	255	19M	=	270	286	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	255	19M	=	3	-286	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	205	255	19M	=	270	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	255	19M	=	205	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	255	19M	=	68	84	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	68	255	19M	=	3	-84	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	104	255	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	270	255	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	355	0	3	255	19M	=	169	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	403	0	169	255	19M	=	3	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	83	0	379	255	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
r2	163	0	307	255	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
Mate reporting order, -M 1 (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2   --large-index  --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	99	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	147	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	83	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	163	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	99	0	307	42	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
r2	147	0	379	42	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
Mate reporting order, -M 1 (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2   --large-index  --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:407
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0	83	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	163	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	99	0	104	1	19M	=	270	185	CTATCATCACGCGGATATT	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r1	147	0	270	1	19M	=	104	-185	TTAGGGGTAGACCCCCCCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r2	83	0	379	42	26M	=	307	-98	AAAACGCTCTAGTCAGCTCATTGGCT	IIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:26	YS:i:0	YT:Z:CP
r2	163	0	307	42	30M	=	379	98	ATACGGCCATCGCGGCGGCATTACTCGGCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YS:i:0	YT:Z:CP
Non-overlapping; no args (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index  --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index  --ff --quiet -M 1 --no-discordant --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index  --ff --quiet -M 1 --no-discordant --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index  --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index  --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index  --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index  --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Non-overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
r0	131	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
Non-overlapping; --no-overlap (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	24	42	19M	=	2	-41	CGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:19	YS:i:0	YT:Z:CP
r0	179	0	2	42	18M	=	24	41	GCTATCATCACGCGGATA	IIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:18	YS:i:0	YT:Z:CP
Overlapping; no args (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index  --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index  --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; --no-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-contain (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
r0	131	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
Overlapping; --no-contain (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:CP
r0	179	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:CP
Overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
r0	129	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:DP
Overlapping; --no-overlap (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2   --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	20	42	23M	=	2	-41	TTAGCGCATCGACATTAATATCC	IIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:0	YT:Z:DP
r0	177	0	2	42	21M	=	20	41	GCTATCATCACGCGGATATTA	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
Scoring params 1 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:105
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	42	88M	*	0	0	GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:88	YT:Z:UU
Scoring params 1 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:105
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	42	88M	*	0	0	GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:88	YT:Z:UU
Scoring params 2 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-38	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 2 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-38	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 3 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-31	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 3 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-31	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 4 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-30	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 4 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-30	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 5 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-40	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 5 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-40	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 6 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-41	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Scoring params 6 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2   --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:102
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	37M4D30M3I14M	*	0	0	NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC	GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh	AS:i:-41	XN:i:0	XM:i:2	XO:i:2	XG:i:7	NM:i:9	MD:Z:0G11A24^GACC44	YT:Z:UU
Q XS:i 1a (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-5	XS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-5	XS:i:-5	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,3 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,3 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,6 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a ! --mp 3,6 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII!	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,3 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,3 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,6 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a I --mp 3,6 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1a --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIIA	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-4	XS:i:-4	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-4	XS:i:-4	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1b --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII5	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-3	XS:i:-3	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
Q XS:i 1c --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIII4	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
(fw:1, sam:1)
References:
>0
CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:68
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	73	0	2	255	27M	=	2	0	ATCGACTGAGACTCGTACGACAATTAC	IIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:27	YT:Z:UP
r0	133	0	2	0	*	=	2	0	TAGGTTTCGCGCGAAACGCTGGTGAT	IIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
(fw:0, sam:1)
References:
>0
CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT
./bowtie2   --large-index  --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:68
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	137	0	2	255	27M	=	2	0	ATCGACTGAGACTCGTACGACAATTAC	IIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:27	YT:Z:UP
r0	69	0	2	0	*	=	2	0	TAGGTTTCGCGCGAAACGCTGGTGAT	IIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:528
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	457	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT
./bowtie2   --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:528
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	289	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 1 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
XS:i 1 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-6	XS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:7A0	YT:Z:UU
XS:i 2 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet  --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGT	IIIIIIII	YT:Z:UU
XS:i 2 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet  --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACGAACAA	IIIIIIII	YT:Z:UU
XS:i 3a (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3a (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3b (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3b (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3c (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 3c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2   --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	39	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4a (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2   --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4b (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2   --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 4b (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2   --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:24
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5a (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2   --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5b (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2   --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
XS:i 5b (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2   --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	17	35	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:-6	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
BWA-SW-like 1 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --bwa-sw-like --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:56	YT:Z:UU
BWA-SW-like 1 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2   --large-index --bwa-sw-like --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:56	YT:Z:UU
BWA-SW-like 2 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2   --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:48	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:26A0A28	YT:Z:UU
BWA-SW-like 2 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2   --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	56M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:48	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:26A0A28	YT:Z:UU
BWA-SW-like 3 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2   --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	26M3D27M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:42	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:26^AAC27	YT:Z:UU
BWA-SW-like 3 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2   --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:64
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	26M3D27M	*	0	0	TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:42	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:26^AAC27	YT:Z:UU
SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	147	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2   --large-index  --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	131	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2   --large-index  --rf --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	4	255	24M	=	4	-24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
r0	163	0	4	255	24M	=	4	24	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 1 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2   --large-index  --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	147	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 2 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2   --large-index  --rf --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	163	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where both mates align 3 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2   --large-index  --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGTGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:-6	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:21C2	YS:i:0	YT:Z:CP
r0	131	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:-6	YT:Z:CP
SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2   --large-index  --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	73	0	4	255	24M	=	4	0	CTATCTACGCTTCGGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:24	YT:Z:UP
r0	133	0	4	0	*	=	4	0	GATTGTCTTTTCCCGGAAAAATCGT	IIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
SAM paired-end where neither mate aligns (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2   --large-index  --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CTATATACGAAAAAGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	GATTGTCTTTTCCCGGAAAAATCGT	IIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
SAM paired-end where both mates align, but discordantly (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2   --large-index  --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:69
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	24M	=	36	53	CTATCTACGCTTCGGCGTCGGCGA	IIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:24	YS:i:0	YT:Z:DP
r0	129	0	36	255	21M	=	4	-53	ACGACCGGGTGTGTGACAATC	IIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:21	YS:i:0	YT:Z:DP
matchesRef regression 4 (fw:1, sam:1)
References:
>0
CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC
>1
GCTCGGAATTCGTGCTCCGNCCCGTACGGTT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@SQ	SN:1	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
matchesRef regression 4 (fw:0, sam:1)
References:
>0
CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC
>1
GCTCGGAATTCGTGCTCCGNCCCGTACGGTT
./bowtie2   --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:120
@SQ	SN:1	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UU
matchesRef regression 3 (fw:1, sam:1)
References:
>0
GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	10	255	38M	*	0	0	CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UU
matchesRef regression 3 (fw:0, sam:1)
References:
>0
GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC
./bowtie2   --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	10	255	38M	*	0	0	CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:38	YT:Z:UU
matchesRef regression 2 (fw:1, sam:1)
References:
>0
GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG
>1
CCTTGTTNTTAATGCTGCCTGGTTTNG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@SQ	SN:1	LN:27
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	YT:Z:UP
matchesRef regression 2 (fw:0, sam:1)
References:
>0
GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG
>1
CCTTGTTNTTAATGCTGCCTGGTTTNG
./bowtie2   --large-index --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:47
@SQ	SN:1	LN:27
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	1	255	29S23M	=	1	-68	CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-78	XN:i:7	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:23	YS:i:-128	YT:Z:CP
r0	163	0	1	255	45S15M	=	1	68	CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-128	XN:i:9	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:14T0	YS:i:-78	YT:Z:CP
matchesRef regression 1 (fw:1, sam:1)
References:
>0
AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:61
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	12	255	50M10S	*	0	0	AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:9	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
matchesRef regression 1 (fw:0, sam:1)
References:
>0
AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC
./bowtie2   --large-index --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:61
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	12	255	50M10S	*	0	0	AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:-17	XN:i:9	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:50	YT:Z:UU
Discordant with different chromosomes (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCC
>1
CCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:23
@SQ	SN:1	LN:28
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	65	0	4	255	10M	1	8	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	1	8	255	10M	0	4	0	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	65	0	4	255	10M	1	7	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	129	1	7	255	10M	0	4	0	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Discordant with different chromosomes (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCC
>1
CCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2   --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:23
@SQ	SN:1	LN:28
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	113	1	8	255	10M	0	4	0	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	1	8	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	113	1	7	255	10M	0	4	0	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	177	0	4	255	10M	1	7	0	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r1	99	0	1	255	10M	=	10	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	147	0	10	255	10M	=	1	-19	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r1	83	0	10	255	10M	=	1	-19	CAGTATCTGA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	163	0	1	255	10M	=	10	19	AGCATCGATC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 2 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r1	0	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r1	16	0	4	255	11M	*	0	0	ATCGATCAGTA	IIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:11	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	4	255	9M	*	0	0	ATCGATCAG	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	6	255	9M	*	0	0	CGATCAGTA	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	16	0	4	255	9M	*	0	0	ATCGATCAG	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2   --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:19
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1	0	0	6	255	9M	*	0	0	CGATCAGTA	IIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:9	YT:Z:UU
(fw:1, sam:1)
References:
>0
TGC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:3
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	1S3M	*	0	0	ATGC	IIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
(fw:0, sam:1)
References:
>0
TGC
./bowtie2   --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:3
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	1S3M	*	0	0	ATGC	IIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:3	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index  --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index  --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index  --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index  --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
r2	0	0	1	255	1S6M	*	0	0	ATTGTTC	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
r2	16	0	1	255	1S6M	*	0	0	ATTGTTC	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
r0	0	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r2	4	*	0	0	*	*	0	0	GTTCGTA	IIIIIII	YT:Z:UU
r3	4	*	0	0	*	*	0	0	ATTGTTC	IIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
r0	16	0	2	255	7M	*	0	0	TGTTCGT	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r1	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
r2	4	*	0	0	*	*	0	0	TACGAAC	IIIIIII	YT:Z:UU
r3	4	*	0	0	*	*	0	0	GAACAAT	IIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M	*	0	0	TTGTTCG	IIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:7	YT:Z:UU
P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2   --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2   --large-index -X 1000 --local --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2   --large-index -X 1000 --local --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	961	1	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2   --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	255	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	961	255	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	255	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	553	255	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	255	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	487	255	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	355	0	13	255	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	403	0	724	255	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2   --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	961	255	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	255	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	553	255	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	255	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	487	255	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	255	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	339	0	724	255	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	419	0	13	255	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2   --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	255	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	961	255	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	255	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	553	255	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	255	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	487	255	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	355	0	13	255	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	403	0	724	255	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.58.L.b Unpaired -k 5 w/ 8 hits local, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2   --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1000
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	790	1	28M	=	13	-805	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	1	33M	=	790	805	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	961	255	28M	=	13	-976	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	255	33M	=	961	976	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	553	255	28M	=	13	-568	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	255	33M	=	553	568	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	487	255	28M	=	13	-502	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	255	33M	=	487	502	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	339	0	724	255	28M	=	13	-739	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	419	0	13	255	33M	=	724	739	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	255	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	316	255	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	255	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	250	255	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	255	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	316	255	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	255	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	250	255	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index  --fr --quiet -M 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index  --fr --quiet -M 1 -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index  --fr --quiet -M 1 --local -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index  --fr --quiet -M 1 --local -X 150 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:363
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	316	1	28M	=	250	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	250	1	33M	=	316	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --fr --quiet -k 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index  --fr --quiet -k 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	255	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	255	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	42	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	79	42	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	42	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	13	42	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	13	44	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	79	44	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2   --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:126
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	79	44	28M	=	13	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	13	44	33M	=	79	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:2607
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	1909	1	33M	=	1975	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
r0	147	0	1975	1	28M	=	1909	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA
./bowtie2   --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:2607
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	1975	1	28M	=	1909	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:0	YT:Z:CP
r0	163	0	1909	1	33M	=	1975	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:0	YT:Z:CP
P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1906
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	1672	1	33M	=	1738	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
r0	147	0	1738	1	28M	=	1672	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC
./bowtie2   --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:1906
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	1738	1	28M	=	1672	-94	ACACACCCCTATAGCTCGGAGCTGACTG	IIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:56	XS:i:56	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:28	YS:i:66	YT:Z:CP
r0	163	0	1672	1	33M	=	1738	94	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YS:i:56	YT:Z:CP
U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	42	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	42	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2   --large-index --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	44	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2   --large-index --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	44	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2   --large-index  --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2   --large-index  --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2   --large-index --local --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2   --large-index --local --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:56
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	13	255	33M	*	0	0	CAGCGTACGGTATCTAGCTATGGGCATCGATCG	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:66	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:33	YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -k 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index --local --quiet -k 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:85
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	49	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -X 150 --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index -X 150 --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index --local --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	134	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index --local --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	177	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	134	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	177	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	92	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index  --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	262	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	134	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	92	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	304	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	177	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index --local --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	219	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	134	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	7	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	177	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	256	0	92	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
U.k.58.L. Unpaired -k 5 w/ 8 hits local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2   --large-index --local --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:340
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	262	1	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	134	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	92	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	304	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
r0	272	0	177	255	30M	*	0	0	AGATTACGGATCTACGATTCGAGTCGGTCA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIII	AS:i:60	XS:i:60	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:30	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
r0	256	0	1	255	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	0	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
r0	272	0	1	255	8M	*	0	0	TTGTTCAT	IIIIIIII	AS:i:-27	XS:i:-27	XN:i:0	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:6G1	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCAT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATGAACAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	0	0	24	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	24	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	24	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	24	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	35	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	35	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	35	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	35	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	5	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	5	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	5	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	5	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	31	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	31	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	31	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	31	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2   --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	16	0	10	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	10	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	10	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	10	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	39	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	39	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	39	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	39	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	1	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	1	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	1	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	1	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	43	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	43	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	43	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	43	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
Gap penalties 1 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	6M1D6M	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	AS:i:-39	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^G6	YT:Z:UU
Gap penalties 1 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	6M1D6M	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	AS:i:-39	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:6^G6	YT:Z:UU
Gap penalties 2 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCTTTGTT	IIIIIIIIIIII	YT:Z:UU
Gap penalties 2 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAAGAACAA	IIIIIIIIIIII	YT:Z:UU
Gap penalties 3 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
Gap penalties 3 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
Gap penalties 4 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 4 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAATCGAACAA	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 5 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 5 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	AACAAATCGAACAA	IIIIIIIIIIIIII	YT:Z:UU
Gap penalties 6 (fw:1, sam:1)
References:
>0
ATTGTTCGTTTGTTCGTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:18
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	6M1D5M1I6M	*	0	0	ATTGTTGTTTGATTCGTA	IIIIIIIIIIIIIIIIII	AS:i:-57	XN:i:0	XM:i:0	XO:i:2	XG:i:2	NM:i:2	MD:Z:6^C11	YT:Z:UU
Gap penalties 6 (fw:0, sam:1)
References:
>0
ATTGTTCGTTTGTTCGTA
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:18
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	6M1D5M1I6M	*	0	0	ATTGTTGTTTGATTCGTA	IIIIIIIIIIIIIIIIII	AS:i:-57	XN:i:0	XM:i:0	XO:i:2	XG:i:2	NM:i:2	MD:Z:6^C11	YT:Z:UU
Gap penalties 7 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTGTTGTTTGATTCGT	IIIIIIIIIIIIIIII	YT:Z:UU
Gap penalties 7 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACGAATCAAACAACAA	IIIIIIIIIIIIIIII	YT:Z:UU
N filtering 1 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
N filtering 1 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2   --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:13	YT:Z:UU
N filtering 2 (fw:1, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 2 (fw:0, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2   --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 3 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 3 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2   --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 4 (fw:1, sam:1)
References:
>0
GAGACTTTNTACGCATCGAACTATCGCTCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 4 (fw:0, sam:1)
References:
>0
GAGACTTTNTACGCATCGAACTATCGCTCTA
./bowtie2   --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
N filtering 5 (fw:1, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:2N10	YT:Z:UU
N filtering 5 (fw:0, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2   --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	9	255	13M	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:2N10	YT:Z:UU
N filtering 6 (fw:1, sam:1)
References:
>0
GAGACTTTNTACGCATCGAANTATCGCTCTA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ATACGCATCGAAC	IIIIIIIIIIIII	YT:Z:UU
N filtering 6 (fw:0, sam:1)
References:
>0
GAGACTTTNTACGCATCGAANTATCGCTCTA
./bowtie2   --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:31
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	GTTCGATGCGTAT	IIIIIIIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	9M1I4M	*	0	0	TTTTGTTCGATTTG	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	9M1I4M	*	0	0	TTTTGTTCGATTTG	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:13
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	7M1I6M	*	0	0	TTGTTCGATTTGTT	IIIIIIIIIIIIII	AS:i:-45	XN:i:0	XM:i:0	XO:i:1	XG:i:1	NM:i:1	MD:Z:13	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCA
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	4	255	2M	*	0	0	CA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCA
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	4	255	2M	*	0	0	CA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (1) (fw:1, sam:1)
References:
>0
ACNCA
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	2M	*	0	0	AC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (1) (fw:0, sam:1)
References:
>0
ACNCA
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:5
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	2M	*	0	0	AC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (2) (fw:1, sam:1)
References:
>0
ACNCANNNNNNNNCGNNNNNNNNCG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:25
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
N ceil = 0, 2 legit hits (2) (fw:0, sam:1)
References:
>0
ACNCANNNNNNNNCGNNNNNNNNCG
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:25
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	24	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:37
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	32	1	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	32	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	24	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	272	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r0	256	0	14	255	2M	*	0	0	CG	II	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTYGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0	0	0	1	255	8M	*	0	0	TTGTTGGT	IIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:5N2	YT:Z:UU
r1	0	0	1	255	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:-1	XN:i:1	XM:i:1	XO:i:0	XG:i:0	NM:i:1	MD:Z:5N2	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATAACCTTCG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:10
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	4M2D4M	*	0	0	ATAATTCG	IIIIIIII	AS:i:-15	XN:i:0	XM:i:0	XO:i:1	XG:i:2	NM:i:2	MD:Z:4^CC4	YT:Z:UU
(fw:0, sam:1)
References:
>0
ATAACCTTCG
./bowtie2   --large-index  --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:10
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	4M2D4M	*	0	0	ATAATTCG	IIIIIIII	AS:i:-15	XN:i:0	XM:i:0	XO:i:1	XG:i:2	NM:i:2	MD:Z:4^CC4	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATATGCCCCATGCCCCCCTCCG
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:22
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	255	9M3D10M	*	0	0	ATATGCCCCCCCCCCTCCG	IIIIIIIIIIIIIIIIIII	AS:i:-20	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:9^ATG10	YT:Z:UU
(fw:1, sam:1)
References:
>0
ATATGCCCCATGCCCCCCTCCG
./bowtie2   --large-index  --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:22
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	255	9M3D10M	*	0	0	ATATGCCCCCCCCCCTCCG	IIIIIIIIIIIIIIIIIII	AS:i:-20	XN:i:0	XM:i:0	XO:i:1	XG:i:3	NM:i:3	MD:Z:9^ATG10	YT:Z:UU
Simple paired-end 13 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	65	0	4	255	10M	=	30	36	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	129	0	30	255	10M	=	4	-36	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r2	67	0	4	255	10M	=	29	35	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r2	131	0	29	255	10M	=	4	-35	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	67	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	131	0	28	255	10M	=	4	-34	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r4	65	0	5	255	10M	=	31	36	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r4	129	0	31	255	10M	=	5	-36	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r5	67	0	5	255	10M	=	30	35	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r5	131	0	30	255	10M	=	5	-35	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	67	0	5	255	10M	=	29	34	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	131	0	29	255	10M	=	5	-34	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	67	0	5	255	10M	=	28	33	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	131	0	28	255	10M	=	5	-33	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 13 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC
./bowtie2   --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz"
r0	113	0	31	255	10M	=	4	-37	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	113	0	30	255	10M	=	4	-36	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	177	0	4	255	10M	=	30	36	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r2	115	0	29	255	10M	=	4	-35	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r2	179	0	4	255	10M	=	29	35	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	115	0	28	255	10M	=	4	-34	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r3	179	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r4	113	0	31	255	10M	=	5	-36	GTCGCTACCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r4	177	0	5	255	10M	=	31	36	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r5	115	0	30	255	10M	=	5	-35	TGTCGCTACC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r5	179	0	5	255	10M	=	30	35	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	115	0	29	255	10M	=	5	-34	CTGTCGCTAC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r6	179	0	5	255	10M	=	29	34	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	115	0	28	255	10M	=	5	-33	CCTGTCGCTA	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r7	179	0	5	255	10M	=	28	33	TAAAAATATT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 12 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	GGCCCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	67	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	131	0	28	255	10M	=	4	-34	CCGGGCCCGC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 12 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC
./bowtie2   --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0	113	0	31	255	10M	=	4	-37	GGCCCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r1	115	0	28	255	10M	=	4	-34	CCGGGCCCGC	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r1	179	0	4	255	10M	=	28	34	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 11 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	31	255	10M	=	4	-37	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 11 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2   --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:51
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	31	255	10M	=	4	-37	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	31	37	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 10 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:41
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	65	0	4	255	10M	=	21	27	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	129	0	21	255	10M	=	4	-27	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 10 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2   --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:41
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	113	0	21	255	10M	=	4	-27	CGATCGCCCG	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
r0	177	0	4	255	10M	=	21	27	ATAAAAATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:DP
Simple paired-end 9 (fw:1, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	1	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	60	1	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 9 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2   --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	60	1	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	163	0	4	1	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 8 (fw:1, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	99	0	4	1	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	147	0	60	1	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	355	0	38	255	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	403	0	60	255	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	355	0	20	255	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	403	0	60	255	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 8 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2   --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:81
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	83	0	60	1	10M	=	4	-66	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	163	0	4	1	10M	=	60	66	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	339	0	60	255	10M	=	38	-32	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	419	0	38	255	10M	=	60	32	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	339	0	60	255	10M	=	20	-50	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	419	0	20	255	10M	=	60	50	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 2; no --no-mixed (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	153	0	4	255	10M	=	4	0	ATATATATAT	IIIIIIIIII	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YT:Z:UP
r0	101	0	4	0	*	=	4	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
Simple paired-end 2; --no-mixed (fw:1, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	ATATATATAT	IIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
Simple paired-end 2; --no-mixed (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC
./bowtie2   --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	77	*	0	0	*	*	0	0	CCCCCGGGGG	IIIIIIIIII	YT:Z:UP
r0	141	*	0	0	*	*	0	0	ATATATATAT	IIIIIIIIII	YT:Z:UP
Simple paired-end 1 (fw:1, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	67	0	4	255	10M	=	36	42	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	131	0	36	255	10M	=	4	-42	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
Simple paired-end 1 (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC
./bowtie2   --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:53
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0	115	0	36	255	10M	=	4	-42	CGCGCGCGCG	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
r0	179	0	4	255	10M	=	36	42	ATATATATAT	IIIIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:10	YS:i:0	YT:Z:CP
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	0	0	24	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	24	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	24	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	0	0	24	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	35	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	35	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	35	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	0	0	35	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	5	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	5	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	5	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	0	0	5	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	31	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	31	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	31	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	0	0	31	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2   --large-index  --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:49
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1	16	0	10	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	10	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	10	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r1	16	0	10	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	39	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	39	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	39	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r2	16	0	39	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	1	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	1	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	1	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r3	16	0	1	255	2M	*	0	0	AA	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	43	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	43	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	43	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
r4	16	0	43	255	2M	*	0	0	CC	II	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:2	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index  --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated.  Use -D and -R to adjust effort instead.
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	1	8M	*	0	0	TTGTTCGT	IIIIIIII	AS:i:0	XS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:8	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2   --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:8
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	3	255	6M1S	*	0	0	GTTCGTA	IIIIIII	AS:i:-1	XN:i:1	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:6	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity  .simple_tests.pl.fa .simple_tests.tmp
./bowtie2   --large-index  --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index  --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy SEED=0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy SEED=0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	TTATTAGT	IIIIIIII	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	4	*	0	0	*	*	0	0	ACTAATAA	IIIIIIII	YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	0	0	9	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	256	0	1	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	256	0	5	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-3	XS:i:-2	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:1C0G2T2	YT:Z:UU
r0	256	0	4	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2C0G1T0T0G0	YT:Z:UU
r0	256	0	8	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2T0G1T0C0G0	YT:Z:UU
r0	256	0	6	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:0C0G0T2G0T1	YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2   --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD	VN:1.5	SO:unsorted	GO:query
@SQ	SN:0	LN:16
@PG	ID:bowtie2	PN:bowtie2	VN:2.5.1	CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0	16	0	1	0	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	272	0	9	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-2	XS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:2G2C2	YT:Z:UU
r0	272	0	5	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-3	XS:i:-2	XN:i:0	XM:i:3	XO:i:0	XG:i:0	NM:i:3	MD:Z:1C0G2T2	YT:Z:UU
r0	272	0	6	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:0C0G0T2G0T1	YT:Z:UU
r0	272	0	4	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2C0G1T0T0G0	YT:Z:UU
r0	272	0	8	255	8M	*	0	0	TTATTAGT	IIIIIIII	AS:i:-5	XS:i:-2	XN:i:0	XM:i:5	XO:i:0	XG:i:0	NM:i:5	MD:Z:2T0G1T0C0G0	YT:Z:UU
PASSED
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: bowtie2-2.5.1-5.fc42.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.k5iffU
+ umask 022
+ cd /builddir/build/BUILD/bowtie2-2.5.1-build
+ cd bowtie2-2.5.1
+ DOCDIR=/builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2
+ cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/AUTHORS /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2
+ cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/MANUAL /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2
+ cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/MANUAL.markdown /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2
+ cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/NEWS /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2
+ cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/TUTORIAL /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.rdjJDD
+ umask 022
+ cd /builddir/build/BUILD/bowtie2-2.5.1-build
+ cd bowtie2-2.5.1
+ LICENSEDIR=/builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/licenses/bowtie2
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/licenses/bowtie2
+ cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/LICENSE /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/licenses/bowtie2
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: bowtie2 = 2.5.1-5.fc42 bowtie2(x86-64) = 2.5.1-5.fc42 bundled(tiny-thread) = 1.1
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/perl /usr/bin/python3 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.2)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0.2)(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) libz.so.1(ZLIB_1.2.3.5)(64bit) perl(Config) perl(File::Spec) perl(Getopt::Long) perl(POSIX) perl(Sys::Hostname) perl(strict) perl(warnings) rtld(GNU_HASH)
Processing files: bowtie2-debugsource-2.5.1-5.fc42.x86_64
Provides: bowtie2-debugsource = 2.5.1-5.fc42 bowtie2-debugsource(x86-64) = 2.5.1-5.fc42
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: bowtie2-debuginfo-2.5.1-5.fc42.x86_64
Provides: bowtie2-debuginfo = 2.5.1-5.fc42 bowtie2-debuginfo(x86-64) = 2.5.1-5.fc42 debuginfo(build-id) = 10356a5bb6ab69e78504f273c50a89611658238e debuginfo(build-id) = 46e7a22c1f46afe47f46e6dd3c9f7179a9c38875 debuginfo(build-id) = 8db4a4a30ace27adf5f872175d82f3908826ee3b debuginfo(build-id) = 91b960824940cba9be28a238882e34c177a0b46f debuginfo(build-id) = 9f7447c6c1a1f88f4434f8fd2183d9b5df31c350 debuginfo(build-id) = dfff850e1ba91181fb13c88e3990f25c80f8104f
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: bowtie2-debugsource(x86-64) = 2.5.1-5.fc42
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT
Wrote: /builddir/build/RPMS/bowtie2-2.5.1-5.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/bowtie2-debugsource-2.5.1-5.fc42.x86_64.rpm
Wrote: /builddir/build/RPMS/bowtie2-debuginfo-2.5.1-5.fc42.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.AxFeYN
+ umask 022
+ cd /builddir/build/BUILD/bowtie2-2.5.1-build
+ test -d /builddir/build/BUILD/bowtie2-2.5.1-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bowtie2-2.5.1-build
+ rm -rf /builddir/build/BUILD/bowtie2-2.5.1-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild bowtie2-2.5.1-5.fc42.src.rpm
Finish: build phase for bowtie2-2.5.1-5.fc42.src.rpm
INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-x86_64-1727276439.052334/root/var/log/dnf5.log
INFO: Done(/var/lib/copr-rpmbuild/results/bowtie2-2.5.1-5.fc42.src.rpm) Config(child) 5 minutes 13 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "bowtie2",
            "epoch": null,
            "version": "2.5.1",
            "release": "5.fc42",
            "arch": "src"
        },
        {
            "name": "bowtie2",
            "epoch": null,
            "version": "2.5.1",
            "release": "5.fc42",
            "arch": "x86_64"
        },
        {
            "name": "bowtie2-debugsource",
            "epoch": null,
            "version": "2.5.1",
            "release": "5.fc42",
            "arch": "x86_64"
        },
        {
            "name": "bowtie2-debuginfo",
            "epoch": null,
            "version": "2.5.1",
            "release": "5.fc42",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished