Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c109' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5525706 --chroot fedora-rawhide-x86_64 --detached Version: 0.64 PID: 5839 Logging PID: 5840 Task: {'appstream': False, 'background': True, 'build_id': 5525706, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': '9c7fd46cbe8981e3b55f1b6e36f114299ca3b68d', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/codonell/tbb-f39-update/bowtie2', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'bowtie2', 'package_version': '2.4.1-6', 'project_dirname': 'tbb-f39-update', 'project_name': 'tbb-f39-update', 'project_owner': 'codonell', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/codonell/tbb-f39-update/fedora-rawhide-x86_64/', 'id': 'copr_base', 'name': 'Copr repository'}], 'sandbox': 'codonell/tbb-f39-update--codonell', 'source_json': {}, 'source_type': None, 'submitter': 'codonell', 'tags': [], 'task_id': '5525706-fedora-rawhide-x86_64', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/codonell/tbb-f39-update/bowtie2 /var/lib/copr-rpmbuild/workspace/workdir-j9g64gno/bowtie2 --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/codonell/tbb-f39-update/bowtie2', '/var/lib/copr-rpmbuild/workspace/workdir-j9g64gno/bowtie2', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-j9g64gno/bowtie2'... Running: git checkout 9c7fd46cbe8981e3b55f1b6e36f114299ca3b68d cmd: ['git', 'checkout', '9c7fd46cbe8981e3b55f1b6e36f114299ca3b68d'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-j9g64gno/bowtie2 rc: 0 stdout: stderr: Note: switching to '9c7fd46cbe8981e3b55f1b6e36f114299ca3b68d'. 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 9c7fd46 automatic import of bowtie2 Running: copr-distgit-client sources cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-j9g64gno/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 v2.4.1.tar.gz INFO: Calling: curl -H Pragma: -o v2.4.1.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/codonell/tbb-f39-update/bowtie2/v2.4.1.tar.gz/md5/5938482fab363c6356f9662cce38f99c/v2.4.1.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 10.0M 100 10.0M 0 0 50.2M 0 --:--:-- --:--:-- --:--:-- 50.2M INFO: Reading stdout from command: md5sum v2.4.1.tar.gz /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-j9g64gno/bowtie2/bowtie2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-j9g64gno/bowtie2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1676384685.626650 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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-j9g64gno/bowtie2/bowtie2.spec) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1676384685.626650/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Start(bootstrap): dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 492 kB/s | 116 kB 00:00 fedora 2.3 MB/s | 65 MB 00:28 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing: dnf noarch 4.14.0-2.fc38 fedora 478 k dnf-plugins-core noarch 4.3.1-2.fc38 fedora 33 k Installing dependencies: alternatives x86_64 1.21-2.fc38 fedora 38 k audit-libs x86_64 3.1-2.fc39 fedora 117 k basesystem noarch 11-15.fc38 fedora 7.0 k bash x86_64 5.2.15-3.fc38 fedora 1.8 M bzip2-libs x86_64 1.0.8-13.fc38 fedora 41 k ca-certificates noarch 2023.2.60-2.fc38 fedora 845 k coreutils x86_64 9.1-11.fc38 fedora 1.1 M coreutils-common x86_64 9.1-11.fc38 fedora 2.0 M crypto-policies noarch 20221215-2.gita4c31a3.fc38 fedora 90 k curl x86_64 7.87.0-4.fc38 fedora 347 k cyrus-sasl-lib x86_64 2.1.28-9.fc38 fedora 794 k dbus-libs x86_64 1:1.14.6-1.fc38 fedora 156 k dnf-data noarch 4.14.0-2.fc38 fedora 40 k elfutils-default-yama-scope noarch 0.188-5.fc38 fedora 16 k elfutils-libelf x86_64 0.188-5.fc38 fedora 197 k elfutils-libs x86_64 0.188-5.fc38 fedora 259 k expat x86_64 2.5.0-2.fc38 fedora 110 k fedora-gpg-keys noarch 39-0.1 fedora 126 k fedora-release noarch 39-0.1 fedora 12 k fedora-release-common noarch 39-0.1 fedora 22 k fedora-release-identity-basic noarch 39-0.1 fedora 13 k fedora-repos noarch 39-0.1 fedora 9.4 k fedora-repos-rawhide noarch 39-0.1 fedora 9.0 k file-libs x86_64 5.44-2.fc39 fedora 730 k filesystem x86_64 3.18-3.fc38 fedora 1.1 M findutils x86_64 1:4.9.0-3.fc38 fedora 492 k gawk x86_64 5.1.1-5.fc38 fedora 1.0 M gdbm-libs x86_64 1:1.23-3.fc38 fedora 56 k glib2 x86_64 2.75.3-1.fc39 fedora 2.8 M glibc x86_64 2.37-1.fc38 fedora 2.1 M glibc-common x86_64 2.37-1.fc38 fedora 313 k glibc-minimal-langpack x86_64 2.37-1.fc38 fedora 35 k gmp x86_64 1:6.2.1-4.fc38 fedora 313 k gnupg2 x86_64 2.4.0-2.fc38 fedora 2.6 M gnutls x86_64 3.7.8-11.fc38 fedora 1.1 M gpgme x86_64 1.17.1-3.fc38 fedora 210 k grep x86_64 3.8-3.fc38 fedora 293 k ima-evm-utils x86_64 1.4-7.fc38 fedora 62 k json-c x86_64 0.16-4.fc38 fedora 41 k keyutils-libs x86_64 1.6.1-6.fc38 fedora 31 k krb5-libs x86_64 1.20.1-9.fc39 fedora 727 k libacl x86_64 2.3.1-6.fc38 fedora 23 k libarchive x86_64 3.6.1-5.fc39 fedora 400 k libassuan x86_64 2.5.5-6.fc38 fedora 67 k libattr x86_64 2.5.1-6.fc38 fedora 18 k libb2 x86_64 0.98.1-8.fc38 fedora 25 k libblkid x86_64 2.38.1-4.fc38 fedora 106 k libbrotli x86_64 1.0.9-11.fc38 fedora 317 k libcap x86_64 2.48-6.fc38 fedora 67 k libcap-ng x86_64 0.8.3-5.fc38 fedora 32 k libcom_err x86_64 1.46.5-4.fc38 fedora 26 k libcomps x86_64 0.1.18-5.fc38 fedora 77 k libcurl x86_64 7.87.0-4.fc38 fedora 304 k libdnf x86_64 0.68.0-2.fc38 fedora 662 k libevent x86_64 2.1.12-8.fc38 fedora 257 k libffi x86_64 3.4.4-2.fc38 fedora 38 k libfsverity x86_64 1.4-9.fc38 fedora 19 k libgcc x86_64 13.0.1-0.2.fc38 fedora 95 k libgcrypt x86_64 1.10.1-7.fc38 fedora 511 k libgomp x86_64 13.0.1-0.2.fc38 fedora 302 k libgpg-error x86_64 1.46-2.fc38 fedora 228 k libidn2 x86_64 2.3.4-2.fc38 fedora 160 k libksba x86_64 1.6.3-2.fc38 fedora 159 k libmodulemd x86_64 2.14.0-5.fc38 fedora 233 k libmount x86_64 2.38.1-4.fc38 fedora 135 k libnghttp2 x86_64 1.51.0-2.fc38 fedora 75 k libnsl2 x86_64 2.0.0-5.fc38 fedora 30 k libpsl x86_64 0.21.2-2.fc38 fedora 65 k librepo x86_64 1.15.1-2.fc38 fedora 96 k libreport-filesystem noarch 2.17.6-2.fc38 fedora 14 k libselinux x86_64 3.5-0.rc2.1.fc38.1 fedora 87 k libsemanage x86_64 3.5-0.rc2.1.fc38.1 fedora 120 k libsepol x86_64 3.5-0.rc2.1.fc38.1 fedora 324 k libsigsegv x86_64 2.14-4.fc38 fedora 27 k libsmartcols x86_64 2.38.1-4.fc38 fedora 64 k libsolv x86_64 0.7.22-4.fc38 fedora 412 k libssh x86_64 0.10.4-3.fc38 fedora 209 k libssh-config noarch 0.10.4-3.fc38 fedora 8.9 k libstdc++ x86_64 13.0.1-0.2.fc38 fedora 845 k libtasn1 x86_64 4.19.0-2.fc38 fedora 74 k libtirpc x86_64 1.3.3-1.fc38 fedora 94 k libunistring1.0 x86_64 1.0-1.fc38 fedora 539 k libuuid x86_64 2.38.1-4.fc38 fedora 28 k libverto x86_64 0.3.2-5.fc38 fedora 21 k libxcrypt x86_64 4.4.33-7.fc39 fedora 120 k libxml2 x86_64 2.10.3-3.fc38 fedora 700 k libyaml x86_64 0.2.5-9.fc38 fedora 59 k libzstd x86_64 1.5.4-1.fc39 fedora 302 k lua-libs x86_64 5.4.4-8.fc38 fedora 133 k lz4-libs x86_64 1.9.4-2.fc38 fedora 67 k mpdecimal x86_64 2.5.1-6.fc38 fedora 89 k mpfr x86_64 4.1.1-3.fc38 fedora 600 k ncurses-base noarch 6.4-3.20230114.fc38 fedora 87 k ncurses-libs x86_64 6.4-3.20230114.fc38 fedora 333 k nettle x86_64 3.8-3.fc38 fedora 412 k npth x86_64 1.6-12.fc38 fedora 24 k openldap x86_64 2.6.3-2.fc38 fedora 254 k openssl-libs x86_64 1:3.0.8-1.fc39 fedora 2.1 M p11-kit x86_64 0.24.1-6.fc38 fedora 359 k p11-kit-trust x86_64 0.24.1-6.fc38 fedora 136 k pcre2 x86_64 10.42-1.fc38.1 fedora 234 k pcre2-syntax noarch 10.42-1.fc38.1 fedora 144 k popt x86_64 1.19-2.fc38 fedora 67 k publicsuffix-list-dafsa noarch 20221208-2.fc38 fedora 59 k python-pip-wheel noarch 22.3.1-2.fc38 fedora 1.4 M python-setuptools-wheel noarch 65.5.1-2.fc38 fedora 715 k python3 x86_64 3.11.2-1.fc39 fedora 28 k python3-dateutil noarch 1:2.8.2-5.fc38 fedora 360 k python3-dbus x86_64 1.3.2-2.fc38 fedora 157 k python3-distro noarch 1.8.0-3.fc39 fedora 49 k python3-dnf noarch 4.14.0-2.fc38 fedora 604 k python3-dnf-plugins-core noarch 4.3.1-2.fc38 fedora 277 k python3-gpg x86_64 1.17.1-3.fc38 fedora 296 k python3-hawkey x86_64 0.68.0-2.fc38 fedora 108 k python3-libcomps x86_64 0.1.18-5.fc38 fedora 47 k python3-libdnf x86_64 0.68.0-2.fc38 fedora 823 k python3-libs x86_64 3.11.2-1.fc39 fedora 9.6 M python3-rpm x86_64 4.18.0-10.fc38 fedora 72 k python3-six noarch 1.16.0-9.fc38 fedora 42 k readline x86_64 8.2-3.fc38 fedora 212 k rpm x86_64 4.18.0-10.fc38 fedora 569 k rpm-build-libs x86_64 4.18.0-10.fc38 fedora 94 k rpm-libs x86_64 4.18.0-10.fc38 fedora 312 k rpm-sequoia x86_64 1.2.0-3.fc38 fedora 841 k rpm-sign-libs x86_64 4.18.0-10.fc38 fedora 26 k sed x86_64 4.8-12.fc38 fedora 306 k setup noarch 2.14.3-2.fc38 fedora 152 k shadow-utils x86_64 2:4.13-4.fc38 fedora 1.3 M sqlite-libs x86_64 3.40.1-2.fc38 fedora 666 k systemd-libs x86_64 253~rc3-1.fc39 fedora 653 k tpm2-tss x86_64 4.0.1-3.fc38 fedora 675 k tzdata noarch 2022g-2.fc38 fedora 716 k xz-libs x86_64 5.4.1-1.fc38 fedora 108 k zchunk-libs x86_64 1.2.3-2.fc38 fedora 51 k zlib x86_64 1.2.13-3.fc38 fedora 95 k Transaction Summary ================================================================================ Install 137 Packages Total download size: 57 M Installed size: 200 M Downloading Packages: (1/137): basesystem-11-15.fc38.noarch.rpm 21 kB/s | 7.0 kB 00:00 (2/137): alternatives-1.21-2.fc38.x86_64.rpm 83 kB/s | 38 kB 00:00 (3/137): bzip2-libs-1.0.8-13.fc38.x86_64.rpm 437 kB/s | 41 kB 00:00 (4/137): audit-libs-3.1-2.fc39.x86_64.rpm 195 kB/s | 117 kB 00:00 (5/137): ca-certificates-2023.2.60-2.fc38.noarc 2.4 MB/s | 845 kB 00:00 (6/137): coreutils-9.1-11.fc38.x86_64.rpm 2.8 MB/s | 1.1 MB 00:00 (7/137): bash-5.2.15-3.fc38.x86_64.rpm 2.7 MB/s | 1.8 MB 00:00 (8/137): crypto-policies-20221215-2.gita4c31a3. 865 kB/s | 90 kB 00:00 (9/137): curl-7.87.0-4.fc38.x86_64.rpm 2.9 MB/s | 347 kB 00:00 (10/137): dbus-libs-1.14.6-1.fc38.x86_64.rpm 1.5 MB/s | 156 kB 00:00 (11/137): cyrus-sasl-lib-2.1.28-9.fc38.x86_64.r 4.4 MB/s | 794 kB 00:00 (12/137): dnf-data-4.14.0-2.fc38.noarch.rpm 390 kB/s | 40 kB 00:00 (13/137): coreutils-common-9.1-11.fc38.x86_64.r 4.2 MB/s | 2.0 MB 00:00 (14/137): dnf-4.14.0-2.fc38.noarch.rpm 2.8 MB/s | 478 kB 00:00 (15/137): elfutils-default-yama-scope-0.188-5.f 176 kB/s | 16 kB 00:00 (16/137): dnf-plugins-core-4.3.1-2.fc38.noarch. 323 kB/s | 33 kB 00:00 (17/137): elfutils-libelf-0.188-5.fc38.x86_64.r 1.8 MB/s | 197 kB 00:00 (18/137): elfutils-libs-0.188-5.fc38.x86_64.rpm 2.3 MB/s | 259 kB 00:00 (19/137): expat-2.5.0-2.fc38.x86_64.rpm 940 kB/s | 110 kB 00:00 (20/137): fedora-gpg-keys-39-0.1.noarch.rpm 895 kB/s | 126 kB 00:00 (21/137): fedora-release-39-0.1.noarch.rpm 135 kB/s | 12 kB 00:00 (22/137): fedora-release-common-39-0.1.noarch.r 139 kB/s | 22 kB 00:00 (23/137): fedora-repos-39-0.1.noarch.rpm 97 kB/s | 9.4 kB 00:00 (24/137): fedora-release-identity-basic-39-0.1. 94 kB/s | 13 kB 00:00 (25/137): fedora-repos-rawhide-39-0.1.noarch.rp 100 kB/s | 9.0 kB 00:00 (26/137): file-libs-5.44-2.fc39.x86_64.rpm 3.2 MB/s | 730 kB 00:00 (27/137): findutils-4.9.0-3.fc38.x86_64.rpm 2.9 MB/s | 492 kB 00:00 (28/137): filesystem-3.18-3.fc38.x86_64.rpm 4.2 MB/s | 1.1 MB 00:00 (29/137): gdbm-libs-1.23-3.fc38.x86_64.rpm 617 kB/s | 56 kB 00:00 (30/137): gawk-5.1.1-5.fc38.x86_64.rpm 4.0 MB/s | 1.0 MB 00:00 (31/137): glibc-common-2.37-1.fc38.x86_64.rpm 2.9 MB/s | 313 kB 00:00 (32/137): glibc-minimal-langpack-2.37-1.fc38.x8 323 kB/s | 35 kB 00:00 (33/137): glib2-2.75.3-1.fc39.x86_64.rpm 5.9 MB/s | 2.8 MB 00:00 (34/137): glibc-2.37-1.fc38.x86_64.rpm 5.0 MB/s | 2.1 MB 00:00 (35/137): gmp-6.2.1-4.fc38.x86_64.rpm 3.1 MB/s | 313 kB 00:00 (36/137): gpgme-1.17.1-3.fc38.x86_64.rpm 1.8 MB/s | 210 kB 00:00 (37/137): grep-3.8-3.fc38.x86_64.rpm 2.6 MB/s | 293 kB 00:00 (38/137): gnutls-3.7.8-11.fc38.x86_64.rpm 3.1 MB/s | 1.1 MB 00:00 (39/137): ima-evm-utils-1.4-7.fc38.x86_64.rpm 638 kB/s | 62 kB 00:00 (40/137): gnupg2-2.4.0-2.fc38.x86_64.rpm 6.4 MB/s | 2.6 MB 00:00 (41/137): json-c-0.16-4.fc38.x86_64.rpm 429 kB/s | 41 kB 00:00 (42/137): keyutils-libs-1.6.1-6.fc38.x86_64.rpm 330 kB/s | 31 kB 00:00 (43/137): libacl-2.3.1-6.fc38.x86_64.rpm 230 kB/s | 23 kB 00:00 (44/137): krb5-libs-1.20.1-9.fc39.x86_64.rpm 4.2 MB/s | 727 kB 00:00 (45/137): libarchive-3.6.1-5.fc39.x86_64.rpm 3.4 MB/s | 400 kB 00:00 (46/137): libassuan-2.5.5-6.fc38.x86_64.rpm 721 kB/s | 67 kB 00:00 (47/137): libattr-2.5.1-6.fc38.x86_64.rpm 148 kB/s | 18 kB 00:00 (48/137): libb2-0.98.1-8.fc38.x86_64.rpm 199 kB/s | 25 kB 00:00 (49/137): libblkid-2.38.1-4.fc38.x86_64.rpm 1.1 MB/s | 106 kB 00:00 (50/137): libbrotli-1.0.9-11.fc38.x86_64.rpm 2.3 MB/s | 317 kB 00:00 (51/137): libcap-2.48-6.fc38.x86_64.rpm 505 kB/s | 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-------------------------------------------------------------------------------- Total 1.9 MB/s | 57 MB 00:30 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary (0x18B8E74C) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-3.fc38.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.0.1-0.2.fc38.x86_64 1/137 Running scriptlet: libgcc-13.0.1-0.2.fc38.x86_64 1/137 Installing : tzdata-2022g-2.fc38.noarch 2/137 Installing : crypto-policies-20221215-2.gita4c31a3.fc38.noarc 3/137 Running scriptlet: crypto-policies-20221215-2.gita4c31a3.fc38.noarc 3/137 Installing : fedora-release-identity-basic-39-0.1.noarch 4/137 Installing : python-setuptools-wheel-65.5.1-2.fc38.noarch 5/137 Installing : publicsuffix-list-dafsa-20221208-2.fc38.noarch 6/137 Installing : pcre2-syntax-10.42-1.fc38.1.noarch 7/137 Installing : ncurses-base-6.4-3.20230114.fc38.noarch 8/137 Installing : libssh-config-0.10.4-3.fc38.noarch 9/137 Installing : libreport-filesystem-2.17.6-2.fc38.noarch 10/137 Installing : dnf-data-4.14.0-2.fc38.noarch 11/137 warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew Installing : fedora-gpg-keys-39-0.1.noarch 12/137 Installing : 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libcurl-7.87.0-4.fc38.x86_64 120/137 Installing : gnupg2-2.4.0-2.fc38.x86_64 121/137 Installing : gpgme-1.17.1-3.fc38.x86_64 122/137 Installing : librepo-1.15.1-2.fc38.x86_64 123/137 Installing : libdnf-0.68.0-2.fc38.x86_64 124/137 Installing : python3-libdnf-0.68.0-2.fc38.x86_64 125/137 Installing : python3-hawkey-0.68.0-2.fc38.x86_64 126/137 Installing : python3-gpg-1.17.1-3.fc38.x86_64 127/137 Installing : curl-7.87.0-4.fc38.x86_64 128/137 Running scriptlet: tpm2-tss-4.0.1-3.fc38.x86_64 129/137 useradd: Warning: missing or non-executable shell '/usr/sbin/nologin' Installing : tpm2-tss-4.0.1-3.fc38.x86_64 129/137 Installing : ima-evm-utils-1.4-7.fc38.x86_64 130/137 Installing : rpm-sign-libs-4.18.0-10.fc38.x86_64 131/137 Installing : python3-rpm-4.18.0-10.fc38.x86_64 132/137 Installing : python3-dnf-4.14.0-2.fc38.noarch 133/137 Installing : python3-dnf-plugins-core-4.3.1-2.fc38.noarch 134/137 Installing : dnf-plugins-core-4.3.1-2.fc38.noarch 135/137 Installing : dnf-4.14.0-2.fc38.noarch 136/137 Running scriptlet: dnf-4.14.0-2.fc38.noarch 136/137 Running scriptlet: rpm-4.18.0-10.fc38.x86_64 137/137 Installing : rpm-4.18.0-10.fc38.x86_64 137/137 Running scriptlet: filesystem-3.18-3.fc38.x86_64 137/137 Running scriptlet: ca-certificates-2023.2.60-2.fc38.noarch 137/137 Running scriptlet: rpm-4.18.0-10.fc38.x86_64 137/137 Verifying : alternatives-1.21-2.fc38.x86_64 1/137 Verifying : audit-libs-3.1-2.fc39.x86_64 2/137 Verifying : basesystem-11-15.fc38.noarch 3/137 Verifying : bash-5.2.15-3.fc38.x86_64 4/137 Verifying : bzip2-libs-1.0.8-13.fc38.x86_64 5/137 Verifying : ca-certificates-2023.2.60-2.fc38.noarch 6/137 Verifying : coreutils-9.1-11.fc38.x86_64 7/137 Verifying : coreutils-common-9.1-11.fc38.x86_64 8/137 Verifying : crypto-policies-20221215-2.gita4c31a3.fc38.noarc 9/137 Verifying : curl-7.87.0-4.fc38.x86_64 10/137 Verifying : cyrus-sasl-lib-2.1.28-9.fc38.x86_64 11/137 Verifying : dbus-libs-1:1.14.6-1.fc38.x86_64 12/137 Verifying : dnf-4.14.0-2.fc38.noarch 13/137 Verifying : dnf-data-4.14.0-2.fc38.noarch 14/137 Verifying : dnf-plugins-core-4.3.1-2.fc38.noarch 15/137 Verifying : elfutils-default-yama-scope-0.188-5.fc38.noarch 16/137 Verifying : elfutils-libelf-0.188-5.fc38.x86_64 17/137 Verifying : elfutils-libs-0.188-5.fc38.x86_64 18/137 Verifying : expat-2.5.0-2.fc38.x86_64 19/137 Verifying : fedora-gpg-keys-39-0.1.noarch 20/137 Verifying : fedora-release-39-0.1.noarch 21/137 Verifying : fedora-release-common-39-0.1.noarch 22/137 Verifying : fedora-release-identity-basic-39-0.1.noarch 23/137 Verifying : fedora-repos-39-0.1.noarch 24/137 Verifying : fedora-repos-rawhide-39-0.1.noarch 25/137 Verifying : file-libs-5.44-2.fc39.x86_64 26/137 Verifying : filesystem-3.18-3.fc38.x86_64 27/137 Verifying : findutils-1:4.9.0-3.fc38.x86_64 28/137 Verifying : gawk-5.1.1-5.fc38.x86_64 29/137 Verifying : gdbm-libs-1:1.23-3.fc38.x86_64 30/137 Verifying : glib2-2.75.3-1.fc39.x86_64 31/137 Verifying : glibc-2.37-1.fc38.x86_64 32/137 Verifying : glibc-common-2.37-1.fc38.x86_64 33/137 Verifying : glibc-minimal-langpack-2.37-1.fc38.x86_64 34/137 Verifying : gmp-1:6.2.1-4.fc38.x86_64 35/137 Verifying : gnupg2-2.4.0-2.fc38.x86_64 36/137 Verifying : gnutls-3.7.8-11.fc38.x86_64 37/137 Verifying : gpgme-1.17.1-3.fc38.x86_64 38/137 Verifying : grep-3.8-3.fc38.x86_64 39/137 Verifying : ima-evm-utils-1.4-7.fc38.x86_64 40/137 Verifying : json-c-0.16-4.fc38.x86_64 41/137 Verifying : keyutils-libs-1.6.1-6.fc38.x86_64 42/137 Verifying : krb5-libs-1.20.1-9.fc39.x86_64 43/137 Verifying : libacl-2.3.1-6.fc38.x86_64 44/137 Verifying : libarchive-3.6.1-5.fc39.x86_64 45/137 Verifying : libassuan-2.5.5-6.fc38.x86_64 46/137 Verifying : libattr-2.5.1-6.fc38.x86_64 47/137 Verifying : libb2-0.98.1-8.fc38.x86_64 48/137 Verifying : libblkid-2.38.1-4.fc38.x86_64 49/137 Verifying : libbrotli-1.0.9-11.fc38.x86_64 50/137 Verifying : libcap-2.48-6.fc38.x86_64 51/137 Verifying : libcap-ng-0.8.3-5.fc38.x86_64 52/137 Verifying : libcom_err-1.46.5-4.fc38.x86_64 53/137 Verifying : libcomps-0.1.18-5.fc38.x86_64 54/137 Verifying : libcurl-7.87.0-4.fc38.x86_64 55/137 Verifying : libdnf-0.68.0-2.fc38.x86_64 56/137 Verifying : libevent-2.1.12-8.fc38.x86_64 57/137 Verifying : libffi-3.4.4-2.fc38.x86_64 58/137 Verifying : libfsverity-1.4-9.fc38.x86_64 59/137 Verifying : libgcc-13.0.1-0.2.fc38.x86_64 60/137 Verifying : libgcrypt-1.10.1-7.fc38.x86_64 61/137 Verifying : libgomp-13.0.1-0.2.fc38.x86_64 62/137 Verifying : libgpg-error-1.46-2.fc38.x86_64 63/137 Verifying : libidn2-2.3.4-2.fc38.x86_64 64/137 Verifying : libksba-1.6.3-2.fc38.x86_64 65/137 Verifying : libmodulemd-2.14.0-5.fc38.x86_64 66/137 Verifying : libmount-2.38.1-4.fc38.x86_64 67/137 Verifying : libnghttp2-1.51.0-2.fc38.x86_64 68/137 Verifying : libnsl2-2.0.0-5.fc38.x86_64 69/137 Verifying : libpsl-0.21.2-2.fc38.x86_64 70/137 Verifying : librepo-1.15.1-2.fc38.x86_64 71/137 Verifying : libreport-filesystem-2.17.6-2.fc38.noarch 72/137 Verifying : libselinux-3.5-0.rc2.1.fc38.1.x86_64 73/137 Verifying : libsemanage-3.5-0.rc2.1.fc38.1.x86_64 74/137 Verifying : libsepol-3.5-0.rc2.1.fc38.1.x86_64 75/137 Verifying : libsigsegv-2.14-4.fc38.x86_64 76/137 Verifying : libsmartcols-2.38.1-4.fc38.x86_64 77/137 Verifying : libsolv-0.7.22-4.fc38.x86_64 78/137 Verifying : libssh-0.10.4-3.fc38.x86_64 79/137 Verifying : libssh-config-0.10.4-3.fc38.noarch 80/137 Verifying : libstdc++-13.0.1-0.2.fc38.x86_64 81/137 Verifying : libtasn1-4.19.0-2.fc38.x86_64 82/137 Verifying : libtirpc-1.3.3-1.fc38.x86_64 83/137 Verifying : libunistring1.0-1.0-1.fc38.x86_64 84/137 Verifying : libuuid-2.38.1-4.fc38.x86_64 85/137 Verifying : libverto-0.3.2-5.fc38.x86_64 86/137 Verifying : libxcrypt-4.4.33-7.fc39.x86_64 87/137 Verifying : libxml2-2.10.3-3.fc38.x86_64 88/137 Verifying : libyaml-0.2.5-9.fc38.x86_64 89/137 Verifying : libzstd-1.5.4-1.fc39.x86_64 90/137 Verifying : lua-libs-5.4.4-8.fc38.x86_64 91/137 Verifying : lz4-libs-1.9.4-2.fc38.x86_64 92/137 Verifying : mpdecimal-2.5.1-6.fc38.x86_64 93/137 Verifying : mpfr-4.1.1-3.fc38.x86_64 94/137 Verifying : ncurses-base-6.4-3.20230114.fc38.noarch 95/137 Verifying : ncurses-libs-6.4-3.20230114.fc38.x86_64 96/137 Verifying : nettle-3.8-3.fc38.x86_64 97/137 Verifying : npth-1.6-12.fc38.x86_64 98/137 Verifying : openldap-2.6.3-2.fc38.x86_64 99/137 Verifying : openssl-libs-1:3.0.8-1.fc39.x86_64 100/137 Verifying : p11-kit-0.24.1-6.fc38.x86_64 101/137 Verifying : p11-kit-trust-0.24.1-6.fc38.x86_64 102/137 Verifying : pcre2-10.42-1.fc38.1.x86_64 103/137 Verifying : pcre2-syntax-10.42-1.fc38.1.noarch 104/137 Verifying : popt-1.19-2.fc38.x86_64 105/137 Verifying : publicsuffix-list-dafsa-20221208-2.fc38.noarch 106/137 Verifying : python-pip-wheel-22.3.1-2.fc38.noarch 107/137 Verifying : python-setuptools-wheel-65.5.1-2.fc38.noarch 108/137 Verifying : python3-3.11.2-1.fc39.x86_64 109/137 Verifying : python3-dateutil-1:2.8.2-5.fc38.noarch 110/137 Verifying : python3-dbus-1.3.2-2.fc38.x86_64 111/137 Verifying : python3-distro-1.8.0-3.fc39.noarch 112/137 Verifying : python3-dnf-4.14.0-2.fc38.noarch 113/137 Verifying : python3-dnf-plugins-core-4.3.1-2.fc38.noarch 114/137 Verifying : python3-gpg-1.17.1-3.fc38.x86_64 115/137 Verifying : python3-hawkey-0.68.0-2.fc38.x86_64 116/137 Verifying : python3-libcomps-0.1.18-5.fc38.x86_64 117/137 Verifying : python3-libdnf-0.68.0-2.fc38.x86_64 118/137 Verifying : python3-libs-3.11.2-1.fc39.x86_64 119/137 Verifying : python3-rpm-4.18.0-10.fc38.x86_64 120/137 Verifying : python3-six-1.16.0-9.fc38.noarch 121/137 Verifying : readline-8.2-3.fc38.x86_64 122/137 Verifying : rpm-4.18.0-10.fc38.x86_64 123/137 Verifying : rpm-build-libs-4.18.0-10.fc38.x86_64 124/137 Verifying : rpm-libs-4.18.0-10.fc38.x86_64 125/137 Verifying : rpm-sequoia-1.2.0-3.fc38.x86_64 126/137 Verifying : rpm-sign-libs-4.18.0-10.fc38.x86_64 127/137 Verifying : sed-4.8-12.fc38.x86_64 128/137 Verifying : setup-2.14.3-2.fc38.noarch 129/137 Verifying : shadow-utils-2:4.13-4.fc38.x86_64 130/137 Verifying : sqlite-libs-3.40.1-2.fc38.x86_64 131/137 Verifying : systemd-libs-253~rc3-1.fc39.x86_64 132/137 Verifying : tpm2-tss-4.0.1-3.fc38.x86_64 133/137 Verifying : tzdata-2022g-2.fc38.noarch 134/137 Verifying : xz-libs-5.4.1-1.fc38.x86_64 135/137 Verifying : zchunk-libs-1.2.3-2.fc38.x86_64 136/137 Verifying : zlib-1.2.13-3.fc38.x86_64 137/137 Installed products updated. Installed: alternatives-1.21-2.fc38.x86_64 audit-libs-3.1-2.fc39.x86_64 basesystem-11-15.fc38.noarch bash-5.2.15-3.fc38.x86_64 bzip2-libs-1.0.8-13.fc38.x86_64 ca-certificates-2023.2.60-2.fc38.noarch coreutils-9.1-11.fc38.x86_64 coreutils-common-9.1-11.fc38.x86_64 crypto-policies-20221215-2.gita4c31a3.fc38.noarch curl-7.87.0-4.fc38.x86_64 cyrus-sasl-lib-2.1.28-9.fc38.x86_64 dbus-libs-1:1.14.6-1.fc38.x86_64 dnf-4.14.0-2.fc38.noarch dnf-data-4.14.0-2.fc38.noarch dnf-plugins-core-4.3.1-2.fc38.noarch elfutils-default-yama-scope-0.188-5.fc38.noarch elfutils-libelf-0.188-5.fc38.x86_64 elfutils-libs-0.188-5.fc38.x86_64 expat-2.5.0-2.fc38.x86_64 fedora-gpg-keys-39-0.1.noarch fedora-release-39-0.1.noarch fedora-release-common-39-0.1.noarch fedora-release-identity-basic-39-0.1.noarch fedora-repos-39-0.1.noarch fedora-repos-rawhide-39-0.1.noarch file-libs-5.44-2.fc39.x86_64 filesystem-3.18-3.fc38.x86_64 findutils-1:4.9.0-3.fc38.x86_64 gawk-5.1.1-5.fc38.x86_64 gdbm-libs-1:1.23-3.fc38.x86_64 glib2-2.75.3-1.fc39.x86_64 glibc-2.37-1.fc38.x86_64 glibc-common-2.37-1.fc38.x86_64 glibc-minimal-langpack-2.37-1.fc38.x86_64 gmp-1:6.2.1-4.fc38.x86_64 gnupg2-2.4.0-2.fc38.x86_64 gnutls-3.7.8-11.fc38.x86_64 gpgme-1.17.1-3.fc38.x86_64 grep-3.8-3.fc38.x86_64 ima-evm-utils-1.4-7.fc38.x86_64 json-c-0.16-4.fc38.x86_64 keyutils-libs-1.6.1-6.fc38.x86_64 krb5-libs-1.20.1-9.fc39.x86_64 libacl-2.3.1-6.fc38.x86_64 libarchive-3.6.1-5.fc39.x86_64 libassuan-2.5.5-6.fc38.x86_64 libattr-2.5.1-6.fc38.x86_64 libb2-0.98.1-8.fc38.x86_64 libblkid-2.38.1-4.fc38.x86_64 libbrotli-1.0.9-11.fc38.x86_64 libcap-2.48-6.fc38.x86_64 libcap-ng-0.8.3-5.fc38.x86_64 libcom_err-1.46.5-4.fc38.x86_64 libcomps-0.1.18-5.fc38.x86_64 libcurl-7.87.0-4.fc38.x86_64 libdnf-0.68.0-2.fc38.x86_64 libevent-2.1.12-8.fc38.x86_64 libffi-3.4.4-2.fc38.x86_64 libfsverity-1.4-9.fc38.x86_64 libgcc-13.0.1-0.2.fc38.x86_64 libgcrypt-1.10.1-7.fc38.x86_64 libgomp-13.0.1-0.2.fc38.x86_64 libgpg-error-1.46-2.fc38.x86_64 libidn2-2.3.4-2.fc38.x86_64 libksba-1.6.3-2.fc38.x86_64 libmodulemd-2.14.0-5.fc38.x86_64 libmount-2.38.1-4.fc38.x86_64 libnghttp2-1.51.0-2.fc38.x86_64 libnsl2-2.0.0-5.fc38.x86_64 libpsl-0.21.2-2.fc38.x86_64 librepo-1.15.1-2.fc38.x86_64 libreport-filesystem-2.17.6-2.fc38.noarch libselinux-3.5-0.rc2.1.fc38.1.x86_64 libsemanage-3.5-0.rc2.1.fc38.1.x86_64 libsepol-3.5-0.rc2.1.fc38.1.x86_64 libsigsegv-2.14-4.fc38.x86_64 libsmartcols-2.38.1-4.fc38.x86_64 libsolv-0.7.22-4.fc38.x86_64 libssh-0.10.4-3.fc38.x86_64 libssh-config-0.10.4-3.fc38.noarch libstdc++-13.0.1-0.2.fc38.x86_64 libtasn1-4.19.0-2.fc38.x86_64 libtirpc-1.3.3-1.fc38.x86_64 libunistring1.0-1.0-1.fc38.x86_64 libuuid-2.38.1-4.fc38.x86_64 libverto-0.3.2-5.fc38.x86_64 libxcrypt-4.4.33-7.fc39.x86_64 libxml2-2.10.3-3.fc38.x86_64 libyaml-0.2.5-9.fc38.x86_64 libzstd-1.5.4-1.fc39.x86_64 lua-libs-5.4.4-8.fc38.x86_64 lz4-libs-1.9.4-2.fc38.x86_64 mpdecimal-2.5.1-6.fc38.x86_64 mpfr-4.1.1-3.fc38.x86_64 ncurses-base-6.4-3.20230114.fc38.noarch ncurses-libs-6.4-3.20230114.fc38.x86_64 nettle-3.8-3.fc38.x86_64 npth-1.6-12.fc38.x86_64 openldap-2.6.3-2.fc38.x86_64 openssl-libs-1:3.0.8-1.fc39.x86_64 p11-kit-0.24.1-6.fc38.x86_64 p11-kit-trust-0.24.1-6.fc38.x86_64 pcre2-10.42-1.fc38.1.x86_64 pcre2-syntax-10.42-1.fc38.1.noarch popt-1.19-2.fc38.x86_64 publicsuffix-list-dafsa-20221208-2.fc38.noarch python-pip-wheel-22.3.1-2.fc38.noarch python-setuptools-wheel-65.5.1-2.fc38.noarch python3-3.11.2-1.fc39.x86_64 python3-dateutil-1:2.8.2-5.fc38.noarch python3-dbus-1.3.2-2.fc38.x86_64 python3-distro-1.8.0-3.fc39.noarch python3-dnf-4.14.0-2.fc38.noarch python3-dnf-plugins-core-4.3.1-2.fc38.noarch python3-gpg-1.17.1-3.fc38.x86_64 python3-hawkey-0.68.0-2.fc38.x86_64 python3-libcomps-0.1.18-5.fc38.x86_64 python3-libdnf-0.68.0-2.fc38.x86_64 python3-libs-3.11.2-1.fc39.x86_64 python3-rpm-4.18.0-10.fc38.x86_64 python3-six-1.16.0-9.fc38.noarch readline-8.2-3.fc38.x86_64 rpm-4.18.0-10.fc38.x86_64 rpm-build-libs-4.18.0-10.fc38.x86_64 rpm-libs-4.18.0-10.fc38.x86_64 rpm-sequoia-1.2.0-3.fc38.x86_64 rpm-sign-libs-4.18.0-10.fc38.x86_64 sed-4.8-12.fc38.x86_64 setup-2.14.3-2.fc38.noarch shadow-utils-2:4.13-4.fc38.x86_64 sqlite-libs-3.40.1-2.fc38.x86_64 systemd-libs-253~rc3-1.fc39.x86_64 tpm2-tss-4.0.1-3.fc38.x86_64 tzdata-2022g-2.fc38.noarch xz-libs-5.4.1-1.fc38.x86_64 zchunk-libs-1.2.3-2.fc38.x86_64 zlib-1.2.13-3.fc38.x86_64 Complete! Finish(bootstrap): dnf install 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_64-1676384685.626650/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 216 kB/s | 116 kB 00:00 fedora 31 MB/s | 65 MB 00:02 Dependencies resolved. ================================================================================ Package Arch Version Repo Size ================================================================================ Installing group/module packages: bash x86_64 5.2.15-3.fc38 fedora 1.8 M bzip2 x86_64 1.0.8-13.fc38 fedora 52 k coreutils x86_64 9.1-11.fc38 fedora 1.1 M cpio x86_64 2.13-14.fc38 fedora 276 k diffutils x86_64 3.9-1.fc38 fedora 397 k fedora-release-common noarch 39-0.1 fedora 22 k findutils x86_64 1:4.9.0-3.fc38 fedora 492 k gawk x86_64 5.1.1-5.fc38 fedora 1.0 M glibc-minimal-langpack x86_64 2.37-1.fc38 fedora 35 k grep x86_64 3.8-3.fc38 fedora 293 k gzip x86_64 1.12-3.fc38 fedora 166 k info x86_64 7.0.2-1.fc38 fedora 181 k patch x86_64 2.7.6-19.fc38 fedora 126 k redhat-rpm-config noarch 249-1.fc39 fedora 83 k rpm-build x86_64 4.18.0-10.fc38 fedora 77 k sed x86_64 4.8-12.fc38 fedora 306 k shadow-utils x86_64 2:4.13-4.fc38 fedora 1.3 M tar x86_64 2:1.34-7.fc38 fedora 889 k unzip x86_64 6.0-60.fc38 fedora 184 k util-linux x86_64 2.38.1-4.fc38 fedora 2.3 M which x86_64 2.21-37.fc38 fedora 42 k xz x86_64 5.4.1-1.fc38 fedora 419 k Installing dependencies: alternatives x86_64 1.21-2.fc38 fedora 38 k ansible-srpm-macros noarch 1-9.1.fc38 fedora 8.8 k audit-libs x86_64 3.1-2.fc39 fedora 117 k authselect x86_64 1.4.2-2.fc38 fedora 144 k authselect-libs x86_64 1.4.2-2.fc38 fedora 249 k basesystem noarch 11-15.fc38 fedora 7.0 k binutils x86_64 2.39-9.fc38 fedora 5.4 M binutils-gold x86_64 2.39-9.fc38 fedora 784 k bzip2-libs x86_64 1.0.8-13.fc38 fedora 41 k ca-certificates noarch 2023.2.60-2.fc38 fedora 845 k coreutils-common x86_64 9.1-11.fc38 fedora 2.0 M cracklib x86_64 2.9.7-31.fc38 fedora 92 k crypto-policies noarch 20221215-2.gita4c31a3.fc38 fedora 90 k curl x86_64 7.87.0-4.fc38 fedora 347 k cyrus-sasl-lib x86_64 2.1.28-9.fc38 fedora 794 k debugedit x86_64 5.0-7.fc38 fedora 78 k dwz x86_64 0.15-2.fc38 fedora 135 k ed x86_64 1.19-2.fc38 fedora 78 k efi-srpm-macros noarch 5-7.fc38 fedora 22 k elfutils x86_64 0.188-5.fc38 fedora 530 k elfutils-debuginfod-client x86_64 0.188-5.fc38 fedora 40 k elfutils-default-yama-scope noarch 0.188-5.fc38 fedora 16 k elfutils-libelf x86_64 0.188-5.fc38 fedora 197 k elfutils-libs x86_64 0.188-5.fc38 fedora 259 k fedora-gpg-keys noarch 39-0.1 fedora 126 k fedora-release noarch 39-0.1 fedora 12 k fedora-release-identity-basic noarch 39-0.1 fedora 13 k fedora-repos noarch 39-0.1 fedora 9.4 k fedora-repos-rawhide noarch 39-0.1 fedora 9.0 k file x86_64 5.44-2.fc39 fedora 49 k file-libs x86_64 5.44-2.fc39 fedora 730 k filesystem x86_64 3.18-3.fc38 fedora 1.1 M fonts-srpm-macros noarch 1:2.0.5-11.fc38 fedora 26 k fpc-srpm-macros noarch 1.3-7.fc38 fedora 7.8 k gdb-minimal x86_64 12.1-16.fc38 fedora 3.8 M gdbm-libs x86_64 1:1.23-3.fc38 fedora 56 k ghc-srpm-macros noarch 1.6.1-1.fc38 fedora 8.0 k glibc x86_64 2.37-1.fc38 fedora 2.1 M glibc-common x86_64 2.37-1.fc38 fedora 313 k glibc-gconv-extra x86_64 2.37-1.fc38 fedora 1.6 M gmp x86_64 1:6.2.1-4.fc38 fedora 313 k gnat-srpm-macros noarch 6-2.fc38 fedora 8.8 k go-srpm-macros noarch 3.2.0-2.fc38 fedora 27 k jansson x86_64 2.13.1-6.fc38 fedora 44 k kernel-srpm-macros noarch 1.0-16.fc38 fedora 9.3 k keyutils-libs x86_64 1.6.1-6.fc38 fedora 31 k krb5-libs x86_64 1.20.1-9.fc39 fedora 727 k libacl x86_64 2.3.1-6.fc38 fedora 23 k libarchive x86_64 3.6.1-5.fc39 fedora 400 k libattr x86_64 2.5.1-6.fc38 fedora 18 k libblkid x86_64 2.38.1-4.fc38 fedora 106 k libbrotli x86_64 1.0.9-11.fc38 fedora 317 k libcap x86_64 2.48-6.fc38 fedora 67 k libcap-ng x86_64 0.8.3-5.fc38 fedora 32 k libcom_err x86_64 1.46.5-4.fc38 fedora 26 k libcurl x86_64 7.87.0-4.fc38 fedora 304 k libdb x86_64 5.3.28-55.fc38 fedora 758 k libeconf x86_64 0.4.0-5.fc38 fedora 27 k libevent x86_64 2.1.12-8.fc38 fedora 257 k libfdisk x86_64 2.38.1-4.fc38 fedora 161 k libffi x86_64 3.4.4-2.fc38 fedora 38 k libgcc x86_64 13.0.1-0.2.fc38 fedora 95 k libgomp x86_64 13.0.1-0.2.fc38 fedora 302 k libidn2 x86_64 2.3.4-2.fc38 fedora 160 k libmount x86_64 2.38.1-4.fc38 fedora 135 k libnghttp2 x86_64 1.51.0-2.fc38 fedora 75 k libnsl2 x86_64 2.0.0-5.fc38 fedora 30 k libpkgconf x86_64 1.8.0-5.fc38 fedora 35 k libpsl x86_64 0.21.2-2.fc38 fedora 65 k libpwquality x86_64 1.4.5-3.fc38 fedora 119 k libselinux x86_64 3.5-0.rc2.1.fc38.1 fedora 87 k libsemanage x86_64 3.5-0.rc2.1.fc38.1 fedora 120 k libsepol x86_64 3.5-0.rc2.1.fc38.1 fedora 324 k libsigsegv x86_64 2.14-4.fc38 fedora 27 k libsmartcols x86_64 2.38.1-4.fc38 fedora 64 k libssh x86_64 0.10.4-3.fc38 fedora 209 k libssh-config noarch 0.10.4-3.fc38 fedora 8.9 k libstdc++ x86_64 13.0.1-0.2.fc38 fedora 845 k libtasn1 x86_64 4.19.0-2.fc38 fedora 74 k libtirpc x86_64 1.3.3-1.fc38 fedora 94 k libunistring1.0 x86_64 1.0-1.fc38 fedora 539 k libutempter x86_64 1.2.1-8.fc38 fedora 26 k libuuid x86_64 2.38.1-4.fc38 fedora 28 k libverto x86_64 0.3.2-5.fc38 fedora 21 k libxcrypt x86_64 4.4.33-7.fc39 fedora 120 k libxml2 x86_64 2.10.3-3.fc38 fedora 700 k libzstd x86_64 1.5.4-1.fc39 fedora 302 k lua-libs x86_64 5.4.4-8.fc38 fedora 133 k lua-srpm-macros noarch 1-8.fc38 fedora 8.6 k lz4-libs x86_64 1.9.4-2.fc38 fedora 67 k mpfr x86_64 4.1.1-3.fc38 fedora 600 k ncurses-base noarch 6.4-3.20230114.fc38 fedora 87 k ncurses-libs x86_64 6.4-3.20230114.fc38 fedora 333 k nettle x86_64 3.8-3.fc38 fedora 412 k nim-srpm-macros noarch 3-8.fc38 fedora 8.5 k ocaml-srpm-macros noarch 7-3.fc38 fedora 13 k openblas-srpm-macros noarch 2-13.fc38 fedora 7.5 k openldap x86_64 2.6.3-2.fc38 fedora 254 k openssl-libs x86_64 1:3.0.8-1.fc39 fedora 2.1 M p11-kit x86_64 0.24.1-6.fc38 fedora 359 k p11-kit-trust x86_64 0.24.1-6.fc38 fedora 136 k package-notes-srpm-macros noarch 0.5-7.fc38 fedora 11 k pam x86_64 1.5.2-16.fc38 fedora 560 k pam-libs x86_64 1.5.2-16.fc38 fedora 58 k pcre2 x86_64 10.42-1.fc38.1 fedora 234 k pcre2-syntax noarch 10.42-1.fc38.1 fedora 144 k perl-srpm-macros noarch 1-48.fc38 fedora 8.4 k pkgconf x86_64 1.8.0-5.fc38 fedora 41 k pkgconf-m4 noarch 1.8.0-5.fc38 fedora 14 k pkgconf-pkg-config x86_64 1.8.0-5.fc38 fedora 9.6 k popt x86_64 1.19-2.fc38 fedora 67 k publicsuffix-list-dafsa noarch 20221208-2.fc38 fedora 59 k pyproject-srpm-macros noarch 1.6.2-1.fc39 fedora 14 k python-srpm-macros noarch 3.11-9.fc38 fedora 26 k qt5-srpm-macros noarch 5.15.8-2.fc38 fedora 8.1 k readline x86_64 8.2-3.fc38 fedora 212 k rpm x86_64 4.18.0-10.fc38 fedora 569 k rpm-build-libs x86_64 4.18.0-10.fc38 fedora 94 k rpm-libs x86_64 4.18.0-10.fc38 fedora 312 k rpm-sequoia x86_64 1.2.0-3.fc38 fedora 841 k rpmautospec-rpm-macros noarch 0.3.5-1.fc38 fedora 9.3 k rust-srpm-macros noarch 23-2.fc38 fedora 9.6 k setup noarch 2.14.3-2.fc38 fedora 152 k sqlite-libs x86_64 3.40.1-2.fc38 fedora 666 k systemd-libs x86_64 253~rc3-1.fc39 fedora 653 k tzdata noarch 2022g-2.fc38 fedora 716 k util-linux-core x86_64 2.38.1-4.fc38 fedora 473 k xxhash-libs x86_64 0.8.1-4.fc38 fedora 40 k xz-libs x86_64 5.4.1-1.fc38 fedora 108 k zip x86_64 3.0-36.fc38 fedora 265 k zlib x86_64 1.2.13-3.fc38 fedora 95 k zstd x86_64 1.5.4-1.fc39 fedora 475 k Installing Groups: Buildsystem building group Transaction Summary ================================================================================ Install 154 Packages Total download size: 53 M Installed size: 182 M Downloading Packages: (1/154): ansible-srpm-macros-1-9.1.fc38.noarch. 30 kB/s | 8.8 kB 00:00 (2/154): alternatives-1.21-2.fc38.x86_64.rpm 120 kB/s | 38 kB 00:00 (3/154): authselect-libs-1.4.2-2.fc38.x86_64.rp 2.0 MB/s | 249 kB 00:00 (4/154): basesystem-11-15.fc38.noarch.rpm 277 kB/s | 7.0 kB 00:00 (5/154): audit-libs-3.1-2.fc39.x86_64.rpm 161 kB/s | 117 kB 00:00 (6/154): authselect-1.4.2-2.fc38.x86_64.rpm 210 kB/s | 144 kB 00:00 (7/154): binutils-gold-2.39-9.fc38.x86_64.rpm 2.3 MB/s | 784 kB 00:00 (8/154): bzip2-1.0.8-13.fc38.x86_64.rpm 2.3 MB/s | 52 kB 00:00 (9/154): bzip2-libs-1.0.8-13.fc38.x86_64.rpm 1.9 MB/s | 41 kB 00:00 (10/154): bash-5.2.15-3.fc38.x86_64.rpm 1.7 MB/s | 1.8 MB 00:01 (11/154): ca-certificates-2023.2.60-2.fc38.noar 4.1 MB/s | 845 kB 00:00 (12/154): coreutils-common-9.1-11.fc38.x86_64.r 5.4 MB/s | 2.0 MB 00:00 (13/154): cpio-2.13-14.fc38.x86_64.rpm 5.9 MB/s | 276 kB 00:00 (14/154): coreutils-9.1-11.fc38.x86_64.rpm 2.3 MB/s | 1.1 MB 00:00 (15/154): cracklib-2.9.7-31.fc38.x86_64.rpm 3.0 MB/s | 92 kB 00:00 (16/154): curl-7.87.0-4.fc38.x86_64.rpm 3.8 MB/s | 347 kB 00:00 (17/154): crypto-policies-20221215-2.gita4c31a3 596 kB/s | 90 kB 00:00 (18/154): debugedit-5.0-7.fc38.x86_64.rpm 1.3 MB/s | 78 kB 00:00 (19/154): cyrus-sasl-lib-2.1.28-9.fc38.x86_64.r 2.5 MB/s | 794 kB 00:00 (20/154): dwz-0.15-2.fc38.x86_64.rpm 1.7 MB/s | 135 kB 00:00 (21/154): ed-1.19-2.fc38.x86_64.rpm 977 kB/s | 78 kB 00:00 (22/154): diffutils-3.9-1.fc38.x86_64.rpm 1.0 MB/s | 397 kB 00:00 (23/154): efi-srpm-macros-5-7.fc38.noarch.rpm 996 kB/s | 22 kB 00:00 (24/154): elfutils-debuginfod-client-0.188-5.fc 916 kB/s | 40 kB 00:00 (25/154): elfutils-default-yama-scope-0.188-5.f 711 kB/s | 16 kB 00:00 (26/154): elfutils-libelf-0.188-5.fc38.x86_64.r 1.1 MB/s | 197 kB 00:00 (27/154): elfutils-0.188-5.fc38.x86_64.rpm 1.8 MB/s | 530 kB 00:00 (28/154): fedora-gpg-keys-39-0.1.noarch.rpm 1.9 MB/s | 126 kB 00:00 (29/154): fedora-release-39-0.1.noarch.rpm 548 kB/s | 12 kB 00:00 (30/154): fedora-release-common-39-0.1.noarch.r 1.0 MB/s | 22 kB 00:00 (31/154): fedora-release-identity-basic-39-0.1. 588 kB/s | 13 kB 00:00 (32/154): fedora-repos-39-0.1.noarch.rpm 438 kB/s | 9.4 kB 00:00 (33/154): elfutils-libs-0.188-5.fc38.x86_64.rpm 1.5 MB/s | 259 kB 00:00 (34/154): fedora-repos-rawhide-39-0.1.noarch.rp 418 kB/s | 9.0 kB 00:00 (35/154): file-5.44-2.fc39.x86_64.rpm 1.1 MB/s | 49 kB 00:00 (36/154): file-libs-5.44-2.fc39.x86_64.rpm 2.4 MB/s | 730 kB 00:00 (37/154): findutils-4.9.0-3.fc38.x86_64.rpm 2.5 MB/s | 492 kB 00:00 (38/154): fonts-srpm-macros-2.0.5-11.fc38.noarc 1.2 MB/s | 26 kB 00:00 (39/154): fpc-srpm-macros-1.3-7.fc38.noarch.rpm 358 kB/s | 7.8 kB 00:00 (40/154): filesystem-3.18-3.fc38.x86_64.rpm 2.0 MB/s | 1.1 MB 00:00 (41/154): gawk-5.1.1-5.fc38.x86_64.rpm 3.1 MB/s | 1.0 MB 00:00 (42/154): gdbm-libs-1.23-3.fc38.x86_64.rpm 2.5 MB/s | 56 kB 00:00 (43/154): ghc-srpm-macros-1.6.1-1.fc38.noarch.r 366 kB/s | 8.0 kB 00:00 (44/154): binutils-2.39-9.fc38.x86_64.rpm 1.6 MB/s | 5.4 MB 00:03 (45/154): glibc-common-2.37-1.fc38.x86_64.rpm 2.8 MB/s | 313 kB 00:00 (46/154): glibc-2.37-1.fc38.x86_64.rpm 3.6 MB/s | 2.1 MB 00:00 (47/154): glibc-minimal-langpack-2.37-1.fc38.x8 1.5 MB/s | 35 kB 00:00 (48/154): gmp-6.2.1-4.fc38.x86_64.rpm 3.0 MB/s | 313 kB 00:00 (49/154): gnat-srpm-macros-6-2.fc38.noarch.rpm 310 kB/s | 8.8 kB 00:00 (50/154): go-srpm-macros-3.2.0-2.fc38.noarch.rp 956 kB/s | 27 kB 00:00 (51/154): glibc-gconv-extra-2.37-1.fc38.x86_64. 3.2 MB/s | 1.6 MB 00:00 (52/154): gzip-1.12-3.fc38.x86_64.rpm 3.1 MB/s | 166 kB 00:00 (53/154): grep-3.8-3.fc38.x86_64.rpm 2.9 MB/s | 293 kB 00:00 (54/154): gdb-minimal-12.1-16.fc38.x86_64.rpm 3.1 MB/s | 3.8 MB 00:01 (55/154): jansson-2.13.1-6.fc38.x86_64.rpm 1.8 MB/s | 44 kB 00:00 (56/154): kernel-srpm-macros-1.0-16.fc38.noarch 423 kB/s | 9.3 kB 00:00 (57/154): keyutils-libs-1.6.1-6.fc38.x86_64.rpm 1.4 MB/s | 31 kB 00:00 (58/154): info-7.0.2-1.fc38.x86_64.rpm 2.7 MB/s | 181 kB 00:00 (59/154): libacl-2.3.1-6.fc38.x86_64.rpm 1.0 MB/s | 23 kB 00:00 (60/154): libattr-2.5.1-6.fc38.x86_64.rpm 794 kB/s | 18 kB 00:00 (61/154): libblkid-2.38.1-4.fc38.x86_64.rpm 2.3 MB/s | 106 kB 00:00 (62/154): libarchive-3.6.1-5.fc39.x86_64.rpm 3.5 MB/s | 400 kB 00:00 (63/154): libcap-2.48-6.fc38.x86_64.rpm 2.9 MB/s | 67 kB 00:00 (64/154): libcap-ng-0.8.3-5.fc38.x86_64.rpm 1.4 MB/s | 32 kB 00:00 (65/154): krb5-libs-1.20.1-9.fc39.x86_64.rpm 4.0 MB/s | 727 kB 00:00 (66/154): libbrotli-1.0.9-11.fc38.x86_64.rpm 3.5 MB/s | 317 kB 00:00 (67/154): libcom_err-1.46.5-4.fc38.x86_64.rpm 1.1 MB/s | 26 kB 00:00 (68/154): libeconf-0.4.0-5.fc38.x86_64.rpm 1.2 MB/s | 27 kB 00:00 (69/154): libcurl-7.87.0-4.fc38.x86_64.rpm 3.3 MB/s | 304 kB 00:00 (70/154): libevent-2.1.12-8.fc38.x86_64.rpm 3.8 MB/s | 257 kB 00:00 (71/154): libffi-3.4.4-2.fc38.x86_64.rpm 1.7 MB/s | 38 kB 00:00 (72/154): libfdisk-2.38.1-4.fc38.x86_64.rpm 3.5 MB/s | 161 kB 00:00 (73/154): libgcc-13.0.1-0.2.fc38.x86_64.rpm 4.1 MB/s | 95 kB 00:00 (74/154): libdb-5.3.28-55.fc38.x86_64.rpm 4.2 MB/s | 758 kB 00:00 (75/154): libidn2-2.3.4-2.fc38.x86_64.rpm 3.5 MB/s | 160 kB 00:00 (76/154): libnghttp2-1.51.0-2.fc38.x86_64.rpm 2.6 MB/s | 75 kB 00:00 (77/154): libmount-2.38.1-4.fc38.x86_64.rpm 2.5 MB/s | 135 kB 00:00 (78/154): libgomp-13.0.1-0.2.fc38.x86_64.rpm 3.1 MB/s | 302 kB 00:00 (79/154): libnsl2-2.0.0-5.fc38.x86_64.rpm 1.3 MB/s | 30 kB 00:00 (80/154): libpkgconf-1.8.0-5.fc38.x86_64.rpm 1.6 MB/s | 35 kB 00:00 (81/154): libpsl-0.21.2-2.fc38.x86_64.rpm 2.8 MB/s | 65 kB 00:00 (82/154): libselinux-3.5-0.rc2.1.fc38.1.x86_64. 3.8 MB/s | 87 kB 00:00 (83/154): libpwquality-1.4.5-3.fc38.x86_64.rpm 2.7 MB/s | 119 kB 00:00 (84/154): libsemanage-3.5-0.rc2.1.fc38.1.x86_64 2.2 MB/s | 120 kB 00:00 (85/154): libsigsegv-2.14-4.fc38.x86_64.rpm 897 kB/s | 27 kB 00:00 (86/154): libsmartcols-2.38.1-4.fc38.x86_64.rpm 2.0 MB/s | 64 kB 00:00 (87/154): libssh-config-0.10.4-3.fc38.noarch.rp 281 kB/s | 8.9 kB 00:00 (88/154): libsepol-3.5-0.rc2.1.fc38.1.x86_64.rp 2.7 MB/s | 324 kB 00:00 (89/154): libssh-0.10.4-3.fc38.x86_64.rpm 2.1 MB/s | 209 kB 00:00 (90/154): libtasn1-4.19.0-2.fc38.x86_64.rpm 2.4 MB/s | 74 kB 00:00 (91/154): libunistring1.0-1.0-1.fc38.x86_64.rpm 2.5 MB/s | 539 kB 00:00 (92/154): libutempter-1.2.1-8.fc38.x86_64.rpm 967 kB/s | 26 kB 00:00 (93/154): libuuid-2.38.1-4.fc38.x86_64.rpm 1.0 MB/s | 28 kB 00:00 (94/154): libverto-0.3.2-5.fc38.x86_64.rpm 834 kB/s | 21 kB 00:00 (95/154): libxcrypt-4.4.33-7.fc39.x86_64.rpm 1.6 MB/s | 120 kB 00:00 (96/154): libstdc++-13.0.1-0.2.fc38.x86_64.rpm 1.6 MB/s | 845 kB 00:00 (97/154): libtirpc-1.3.3-1.fc38.x86_64.rpm 184 kB/s | 94 kB 00:00 (98/154): lua-libs-5.4.4-8.fc38.x86_64.rpm 1.6 MB/s | 133 kB 00:00 (99/154): lua-srpm-macros-1-8.fc38.noarch.rpm 87 kB/s | 8.6 kB 00:00 (100/154): libxml2-2.10.3-3.fc38.x86_64.rpm 2.2 MB/s | 700 kB 00:00 (101/154): libzstd-1.5.4-1.fc39.x86_64.rpm 1.3 MB/s | 302 kB 00:00 (102/154): lz4-libs-1.9.4-2.fc38.x86_64.rpm 1.1 MB/s | 67 kB 00:00 (103/154): ncurses-libs-6.4-3.20230114.fc38.x86 4.0 MB/s | 333 kB 00:00 (104/154): ncurses-base-6.4-3.20230114.fc38.noa 583 kB/s | 87 kB 00:00 (105/154): nettle-3.8-3.fc38.x86_64.rpm 9.2 MB/s | 412 kB 00:00 (106/154): nim-srpm-macros-3-8.fc38.noarch.rpm 395 kB/s | 8.5 kB 00:00 (107/154): ocaml-srpm-macros-7-3.fc38.noarch.rp 622 kB/s | 13 kB 00:00 (108/154): openblas-srpm-macros-2-13.fc38.noarc 326 kB/s | 7.5 kB 00:00 (109/154): openldap-2.6.3-2.fc38.x86_64.rpm 10 MB/s | 254 kB 00:00 (110/154): mpfr-4.1.1-3.fc38.x86_64.rpm 2.5 MB/s | 600 kB 00:00 (111/154): p11-kit-0.24.1-6.fc38.x86_64.rpm 14 MB/s | 359 kB 00:00 (112/154): package-notes-srpm-macros-0.5-7.fc38 373 kB/s | 11 kB 00:00 (113/154): p11-kit-trust-0.24.1-6.fc38.x86_64.r 740 kB/s | 136 kB 00:00 (114/154): pam-libs-1.5.2-16.fc38.x86_64.rpm 2.6 MB/s | 58 kB 00:00 (115/154): pam-1.5.2-16.fc38.x86_64.rpm 3.1 MB/s | 560 kB 00:00 (116/154): patch-2.7.6-19.fc38.x86_64.rpm 5.4 MB/s | 126 kB 00:00 (117/154): pcre2-10.42-1.fc38.1.x86_64.rpm 9.0 MB/s | 234 kB 00:00 (118/154): pcre2-syntax-10.42-1.fc38.1.noarch.r 6.1 MB/s | 144 kB 00:00 (119/154): perl-srpm-macros-1-48.fc38.noarch.rp 292 kB/s | 8.4 kB 00:00 (120/154): pkgconf-1.8.0-5.fc38.x86_64.rpm 1.8 MB/s | 41 kB 00:00 (121/154): pkgconf-m4-1.8.0-5.fc38.noarch.rpm 628 kB/s | 14 kB 00:00 (122/154): openssl-libs-3.0.8-1.fc39.x86_64.rpm 6.5 MB/s | 2.1 MB 00:00 (123/154): pkgconf-pkg-config-1.8.0-5.fc38.x86_ 408 kB/s | 9.6 kB 00:00 (124/154): popt-1.19-2.fc38.x86_64.rpm 2.1 MB/s | 67 kB 00:00 (125/154): publicsuffix-list-dafsa-20221208-2.f 2.0 MB/s | 59 kB 00:00 (126/154): pyproject-srpm-macros-1.6.2-1.fc39.n 489 kB/s | 14 kB 00:00 (127/154): python-srpm-macros-3.11-9.fc38.noarc 1.2 MB/s | 26 kB 00:00 (128/154): qt5-srpm-macros-5.15.8-2.fc38.noarch 378 kB/s | 8.1 kB 00:00 (129/154): readline-8.2-3.fc38.x86_64.rpm 8.6 MB/s | 212 kB 00:00 (130/154): redhat-rpm-config-249-1.fc39.noarch. 3.6 MB/s | 83 kB 00:00 (131/154): rpm-build-4.18.0-10.fc38.x86_64.rpm 3.0 MB/s | 77 kB 00:00 (132/154): rpm-build-libs-4.18.0-10.fc38.x86_64 4.0 MB/s | 94 kB 00:00 (133/154): rpm-libs-4.18.0-10.fc38.x86_64.rpm 12 MB/s | 312 kB 00:00 (134/154): rpm-4.18.0-10.fc38.x86_64.rpm 7.5 MB/s | 569 kB 00:00 (135/154): rpmautospec-rpm-macros-0.3.5-1.fc38. 416 kB/s | 9.3 kB 00:00 (136/154): rpm-sequoia-1.2.0-3.fc38.x86_64.rpm 18 MB/s | 841 kB 00:00 (137/154): rust-srpm-macros-23-2.fc38.noarch.rp 446 kB/s | 9.6 kB 00:00 (138/154): sed-4.8-12.fc38.x86_64.rpm 12 MB/s | 306 kB 00:00 (139/154): setup-2.14.3-2.fc38.noarch.rpm 6.5 MB/s | 152 kB 00:00 (140/154): sqlite-libs-3.40.1-2.fc38.x86_64.rpm 14 MB/s | 666 kB 00:00 (141/154): systemd-libs-253~rc3-1.fc39.x86_64.r 14 MB/s | 653 kB 00:00 (142/154): tar-1.34-7.fc38.x86_64.rpm 28 MB/s | 889 kB 00:00 (143/154): unzip-6.0-60.fc38.x86_64.rpm 7.7 MB/s | 184 kB 00:00 (144/154): tzdata-2022g-2.fc38.noarch.rpm 14 MB/s | 716 kB 00:00 (145/154): shadow-utils-4.13-4.fc38.x86_64.rpm 11 MB/s | 1.3 MB 00:00 (146/154): which-2.21-37.fc38.x86_64.rpm 1.4 MB/s | 42 kB 00:00 (147/154): xxhash-libs-0.8.1-4.fc38.x86_64.rpm 1.8 MB/s | 40 kB 00:00 (148/154): util-linux-2.38.1-4.fc38.x86_64.rpm 32 MB/s | 2.3 MB 00:00 (149/154): xz-libs-5.4.1-1.fc38.x86_64.rpm 4.7 MB/s | 108 kB 00:00 (150/154): xz-5.4.1-1.fc38.x86_64.rpm 9.1 MB/s | 419 kB 00:00 (151/154): zip-3.0-36.fc38.x86_64.rpm 10 MB/s | 265 kB 00:00 (152/154): zlib-1.2.13-3.fc38.x86_64.rpm 4.1 MB/s | 95 kB 00:00 (153/154): zstd-1.5.4-1.fc39.x86_64.rpm 18 MB/s | 475 kB 00:00 (154/154): util-linux-core-2.38.1-4.fc38.x86_64 3.2 MB/s | 473 kB 00:00 -------------------------------------------------------------------------------- Total 7.2 MB/s | 53 MB 00:07 fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x18B8E74C: Userid : "Fedora (39) " Fingerprint: E8F2 3996 F232 1864 0CB4 4CBE 75CF 5AC4 18B8 E74C From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary Key imported successfully fedora 1.6 MB/s | 1.6 kB 00:00 GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-39-primary (0x18B8E74C) is already installed fedora 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0xEB10B464: Userid : "Fedora (38) " Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464 From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.18-3.fc38.x86_64 1/1 Preparing : 1/1 Installing : libgcc-13.0.1-0.2.fc38.x86_64 1/154 Running scriptlet: libgcc-13.0.1-0.2.fc38.x86_64 1/154 Installing : crypto-policies-20221215-2.gita4c31a3.fc38.noarc 2/154 Running scriptlet: crypto-policies-20221215-2.gita4c31a3.fc38.noarc 2/154 Installing : tzdata-2022g-2.fc38.noarch 3/154 Installing : fedora-release-identity-basic-39-0.1.noarch 4/154 Installing : rust-srpm-macros-23-2.fc38.noarch 5/154 Installing : qt5-srpm-macros-5.15.8-2.fc38.noarch 6/154 Installing : pyproject-srpm-macros-1.6.2-1.fc39.noarch 7/154 Installing : publicsuffix-list-dafsa-20221208-2.fc38.noarch 8/154 Installing : pkgconf-m4-1.8.0-5.fc38.noarch 9/154 Installing : perl-srpm-macros-1-48.fc38.noarch 10/154 Installing : pcre2-syntax-10.42-1.fc38.1.noarch 11/154 Installing : package-notes-srpm-macros-0.5-7.fc38.noarch 12/154 Installing : openblas-srpm-macros-2-13.fc38.noarch 13/154 Installing : 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util-linux-2.38.1-4.fc38.x86_64 152/154 Installing : which-2.21-37.fc38.x86_64 153/154 Installing : info-7.0.2-1.fc38.x86_64 154/154 Running scriptlet: filesystem-3.18-3.fc38.x86_64 154/154 Running scriptlet: ca-certificates-2023.2.60-2.fc38.noarch 154/154 Running scriptlet: authselect-libs-1.4.2-2.fc38.x86_64 154/154 Running scriptlet: rpm-4.18.0-10.fc38.x86_64 154/154 Running scriptlet: info-7.0.2-1.fc38.x86_64 154/154 Verifying : alternatives-1.21-2.fc38.x86_64 1/154 Verifying : ansible-srpm-macros-1-9.1.fc38.noarch 2/154 Verifying : audit-libs-3.1-2.fc39.x86_64 3/154 Verifying : authselect-1.4.2-2.fc38.x86_64 4/154 Verifying : authselect-libs-1.4.2-2.fc38.x86_64 5/154 Verifying : basesystem-11-15.fc38.noarch 6/154 Verifying : bash-5.2.15-3.fc38.x86_64 7/154 Verifying : binutils-2.39-9.fc38.x86_64 8/154 Verifying : binutils-gold-2.39-9.fc38.x86_64 9/154 Verifying : bzip2-1.0.8-13.fc38.x86_64 10/154 Verifying : bzip2-libs-1.0.8-13.fc38.x86_64 11/154 Verifying : ca-certificates-2023.2.60-2.fc38.noarch 12/154 Verifying : coreutils-9.1-11.fc38.x86_64 13/154 Verifying : coreutils-common-9.1-11.fc38.x86_64 14/154 Verifying : cpio-2.13-14.fc38.x86_64 15/154 Verifying : cracklib-2.9.7-31.fc38.x86_64 16/154 Verifying : crypto-policies-20221215-2.gita4c31a3.fc38.noarc 17/154 Verifying : curl-7.87.0-4.fc38.x86_64 18/154 Verifying : cyrus-sasl-lib-2.1.28-9.fc38.x86_64 19/154 Verifying : debugedit-5.0-7.fc38.x86_64 20/154 Verifying : diffutils-3.9-1.fc38.x86_64 21/154 Verifying : dwz-0.15-2.fc38.x86_64 22/154 Verifying : ed-1.19-2.fc38.x86_64 23/154 Verifying : efi-srpm-macros-5-7.fc38.noarch 24/154 Verifying : elfutils-0.188-5.fc38.x86_64 25/154 Verifying : elfutils-debuginfod-client-0.188-5.fc38.x86_64 26/154 Verifying : elfutils-default-yama-scope-0.188-5.fc38.noarch 27/154 Verifying : elfutils-libelf-0.188-5.fc38.x86_64 28/154 Verifying : elfutils-libs-0.188-5.fc38.x86_64 29/154 Verifying : fedora-gpg-keys-39-0.1.noarch 30/154 Verifying : fedora-release-39-0.1.noarch 31/154 Verifying : fedora-release-common-39-0.1.noarch 32/154 Verifying : fedora-release-identity-basic-39-0.1.noarch 33/154 Verifying : fedora-repos-39-0.1.noarch 34/154 Verifying : fedora-repos-rawhide-39-0.1.noarch 35/154 Verifying : file-5.44-2.fc39.x86_64 36/154 Verifying : file-libs-5.44-2.fc39.x86_64 37/154 Verifying : filesystem-3.18-3.fc38.x86_64 38/154 Verifying : findutils-1:4.9.0-3.fc38.x86_64 39/154 Verifying : fonts-srpm-macros-1:2.0.5-11.fc38.noarch 40/154 Verifying : fpc-srpm-macros-1.3-7.fc38.noarch 41/154 Verifying : gawk-5.1.1-5.fc38.x86_64 42/154 Verifying : gdb-minimal-12.1-16.fc38.x86_64 43/154 Verifying : gdbm-libs-1:1.23-3.fc38.x86_64 44/154 Verifying : ghc-srpm-macros-1.6.1-1.fc38.noarch 45/154 Verifying : glibc-2.37-1.fc38.x86_64 46/154 Verifying : glibc-common-2.37-1.fc38.x86_64 47/154 Verifying : glibc-gconv-extra-2.37-1.fc38.x86_64 48/154 Verifying : glibc-minimal-langpack-2.37-1.fc38.x86_64 49/154 Verifying : gmp-1:6.2.1-4.fc38.x86_64 50/154 Verifying : gnat-srpm-macros-6-2.fc38.noarch 51/154 Verifying : go-srpm-macros-3.2.0-2.fc38.noarch 52/154 Verifying : grep-3.8-3.fc38.x86_64 53/154 Verifying : gzip-1.12-3.fc38.x86_64 54/154 Verifying : info-7.0.2-1.fc38.x86_64 55/154 Verifying : jansson-2.13.1-6.fc38.x86_64 56/154 Verifying : kernel-srpm-macros-1.0-16.fc38.noarch 57/154 Verifying : keyutils-libs-1.6.1-6.fc38.x86_64 58/154 Verifying : krb5-libs-1.20.1-9.fc39.x86_64 59/154 Verifying : libacl-2.3.1-6.fc38.x86_64 60/154 Verifying : libarchive-3.6.1-5.fc39.x86_64 61/154 Verifying : libattr-2.5.1-6.fc38.x86_64 62/154 Verifying : libblkid-2.38.1-4.fc38.x86_64 63/154 Verifying : libbrotli-1.0.9-11.fc38.x86_64 64/154 Verifying : libcap-2.48-6.fc38.x86_64 65/154 Verifying : libcap-ng-0.8.3-5.fc38.x86_64 66/154 Verifying : libcom_err-1.46.5-4.fc38.x86_64 67/154 Verifying : libcurl-7.87.0-4.fc38.x86_64 68/154 Verifying : libdb-5.3.28-55.fc38.x86_64 69/154 Verifying : libeconf-0.4.0-5.fc38.x86_64 70/154 Verifying : libevent-2.1.12-8.fc38.x86_64 71/154 Verifying : libfdisk-2.38.1-4.fc38.x86_64 72/154 Verifying : libffi-3.4.4-2.fc38.x86_64 73/154 Verifying : libgcc-13.0.1-0.2.fc38.x86_64 74/154 Verifying : libgomp-13.0.1-0.2.fc38.x86_64 75/154 Verifying : libidn2-2.3.4-2.fc38.x86_64 76/154 Verifying : libmount-2.38.1-4.fc38.x86_64 77/154 Verifying : libnghttp2-1.51.0-2.fc38.x86_64 78/154 Verifying : libnsl2-2.0.0-5.fc38.x86_64 79/154 Verifying : libpkgconf-1.8.0-5.fc38.x86_64 80/154 Verifying : libpsl-0.21.2-2.fc38.x86_64 81/154 Verifying : libpwquality-1.4.5-3.fc38.x86_64 82/154 Verifying : libselinux-3.5-0.rc2.1.fc38.1.x86_64 83/154 Verifying : libsemanage-3.5-0.rc2.1.fc38.1.x86_64 84/154 Verifying : libsepol-3.5-0.rc2.1.fc38.1.x86_64 85/154 Verifying : libsigsegv-2.14-4.fc38.x86_64 86/154 Verifying : libsmartcols-2.38.1-4.fc38.x86_64 87/154 Verifying : libssh-0.10.4-3.fc38.x86_64 88/154 Verifying : libssh-config-0.10.4-3.fc38.noarch 89/154 Verifying : libstdc++-13.0.1-0.2.fc38.x86_64 90/154 Verifying : libtasn1-4.19.0-2.fc38.x86_64 91/154 Verifying : libtirpc-1.3.3-1.fc38.x86_64 92/154 Verifying : libunistring1.0-1.0-1.fc38.x86_64 93/154 Verifying : libutempter-1.2.1-8.fc38.x86_64 94/154 Verifying : libuuid-2.38.1-4.fc38.x86_64 95/154 Verifying : libverto-0.3.2-5.fc38.x86_64 96/154 Verifying : libxcrypt-4.4.33-7.fc39.x86_64 97/154 Verifying : libxml2-2.10.3-3.fc38.x86_64 98/154 Verifying : libzstd-1.5.4-1.fc39.x86_64 99/154 Verifying : lua-libs-5.4.4-8.fc38.x86_64 100/154 Verifying : lua-srpm-macros-1-8.fc38.noarch 101/154 Verifying : lz4-libs-1.9.4-2.fc38.x86_64 102/154 Verifying : mpfr-4.1.1-3.fc38.x86_64 103/154 Verifying : ncurses-base-6.4-3.20230114.fc38.noarch 104/154 Verifying : ncurses-libs-6.4-3.20230114.fc38.x86_64 105/154 Verifying : nettle-3.8-3.fc38.x86_64 106/154 Verifying : nim-srpm-macros-3-8.fc38.noarch 107/154 Verifying : ocaml-srpm-macros-7-3.fc38.noarch 108/154 Verifying : openblas-srpm-macros-2-13.fc38.noarch 109/154 Verifying : openldap-2.6.3-2.fc38.x86_64 110/154 Verifying : openssl-libs-1:3.0.8-1.fc39.x86_64 111/154 Verifying : p11-kit-0.24.1-6.fc38.x86_64 112/154 Verifying : p11-kit-trust-0.24.1-6.fc38.x86_64 113/154 Verifying : package-notes-srpm-macros-0.5-7.fc38.noarch 114/154 Verifying : pam-1.5.2-16.fc38.x86_64 115/154 Verifying : pam-libs-1.5.2-16.fc38.x86_64 116/154 Verifying : patch-2.7.6-19.fc38.x86_64 117/154 Verifying : pcre2-10.42-1.fc38.1.x86_64 118/154 Verifying : pcre2-syntax-10.42-1.fc38.1.noarch 119/154 Verifying : perl-srpm-macros-1-48.fc38.noarch 120/154 Verifying : pkgconf-1.8.0-5.fc38.x86_64 121/154 Verifying : pkgconf-m4-1.8.0-5.fc38.noarch 122/154 Verifying : pkgconf-pkg-config-1.8.0-5.fc38.x86_64 123/154 Verifying : popt-1.19-2.fc38.x86_64 124/154 Verifying : publicsuffix-list-dafsa-20221208-2.fc38.noarch 125/154 Verifying : pyproject-srpm-macros-1.6.2-1.fc39.noarch 126/154 Verifying : python-srpm-macros-3.11-9.fc38.noarch 127/154 Verifying : qt5-srpm-macros-5.15.8-2.fc38.noarch 128/154 Verifying : readline-8.2-3.fc38.x86_64 129/154 Verifying : redhat-rpm-config-249-1.fc39.noarch 130/154 Verifying : rpm-4.18.0-10.fc38.x86_64 131/154 Verifying : rpm-build-4.18.0-10.fc38.x86_64 132/154 Verifying : rpm-build-libs-4.18.0-10.fc38.x86_64 133/154 Verifying : rpm-libs-4.18.0-10.fc38.x86_64 134/154 Verifying : rpm-sequoia-1.2.0-3.fc38.x86_64 135/154 Verifying : rpmautospec-rpm-macros-0.3.5-1.fc38.noarch 136/154 Verifying : rust-srpm-macros-23-2.fc38.noarch 137/154 Verifying : sed-4.8-12.fc38.x86_64 138/154 Verifying : setup-2.14.3-2.fc38.noarch 139/154 Verifying : shadow-utils-2:4.13-4.fc38.x86_64 140/154 Verifying : sqlite-libs-3.40.1-2.fc38.x86_64 141/154 Verifying : systemd-libs-253~rc3-1.fc39.x86_64 142/154 Verifying : tar-2:1.34-7.fc38.x86_64 143/154 Verifying : tzdata-2022g-2.fc38.noarch 144/154 Verifying : unzip-6.0-60.fc38.x86_64 145/154 Verifying : util-linux-2.38.1-4.fc38.x86_64 146/154 Verifying : util-linux-core-2.38.1-4.fc38.x86_64 147/154 Verifying : which-2.21-37.fc38.x86_64 148/154 Verifying : xxhash-libs-0.8.1-4.fc38.x86_64 149/154 Verifying : xz-5.4.1-1.fc38.x86_64 150/154 Verifying : xz-libs-5.4.1-1.fc38.x86_64 151/154 Verifying : zip-3.0-36.fc38.x86_64 152/154 Verifying : zlib-1.2.13-3.fc38.x86_64 153/154 Verifying : zstd-1.5.4-1.fc39.x86_64 154/154 Installed: alternatives-1.21-2.fc38.x86_64 ansible-srpm-macros-1-9.1.fc38.noarch audit-libs-3.1-2.fc39.x86_64 authselect-1.4.2-2.fc38.x86_64 authselect-libs-1.4.2-2.fc38.x86_64 basesystem-11-15.fc38.noarch bash-5.2.15-3.fc38.x86_64 binutils-2.39-9.fc38.x86_64 binutils-gold-2.39-9.fc38.x86_64 bzip2-1.0.8-13.fc38.x86_64 bzip2-libs-1.0.8-13.fc38.x86_64 ca-certificates-2023.2.60-2.fc38.noarch coreutils-9.1-11.fc38.x86_64 coreutils-common-9.1-11.fc38.x86_64 cpio-2.13-14.fc38.x86_64 cracklib-2.9.7-31.fc38.x86_64 crypto-policies-20221215-2.gita4c31a3.fc38.noarch curl-7.87.0-4.fc38.x86_64 cyrus-sasl-lib-2.1.28-9.fc38.x86_64 debugedit-5.0-7.fc38.x86_64 diffutils-3.9-1.fc38.x86_64 dwz-0.15-2.fc38.x86_64 ed-1.19-2.fc38.x86_64 efi-srpm-macros-5-7.fc38.noarch elfutils-0.188-5.fc38.x86_64 elfutils-debuginfod-client-0.188-5.fc38.x86_64 elfutils-default-yama-scope-0.188-5.fc38.noarch elfutils-libelf-0.188-5.fc38.x86_64 elfutils-libs-0.188-5.fc38.x86_64 fedora-gpg-keys-39-0.1.noarch fedora-release-39-0.1.noarch fedora-release-common-39-0.1.noarch fedora-release-identity-basic-39-0.1.noarch fedora-repos-39-0.1.noarch fedora-repos-rawhide-39-0.1.noarch file-5.44-2.fc39.x86_64 file-libs-5.44-2.fc39.x86_64 filesystem-3.18-3.fc38.x86_64 findutils-1:4.9.0-3.fc38.x86_64 fonts-srpm-macros-1:2.0.5-11.fc38.noarch fpc-srpm-macros-1.3-7.fc38.noarch gawk-5.1.1-5.fc38.x86_64 gdb-minimal-12.1-16.fc38.x86_64 gdbm-libs-1:1.23-3.fc38.x86_64 ghc-srpm-macros-1.6.1-1.fc38.noarch glibc-2.37-1.fc38.x86_64 glibc-common-2.37-1.fc38.x86_64 glibc-gconv-extra-2.37-1.fc38.x86_64 glibc-minimal-langpack-2.37-1.fc38.x86_64 gmp-1:6.2.1-4.fc38.x86_64 gnat-srpm-macros-6-2.fc38.noarch go-srpm-macros-3.2.0-2.fc38.noarch grep-3.8-3.fc38.x86_64 gzip-1.12-3.fc38.x86_64 info-7.0.2-1.fc38.x86_64 jansson-2.13.1-6.fc38.x86_64 kernel-srpm-macros-1.0-16.fc38.noarch keyutils-libs-1.6.1-6.fc38.x86_64 krb5-libs-1.20.1-9.fc39.x86_64 libacl-2.3.1-6.fc38.x86_64 libarchive-3.6.1-5.fc39.x86_64 libattr-2.5.1-6.fc38.x86_64 libblkid-2.38.1-4.fc38.x86_64 libbrotli-1.0.9-11.fc38.x86_64 libcap-2.48-6.fc38.x86_64 libcap-ng-0.8.3-5.fc38.x86_64 libcom_err-1.46.5-4.fc38.x86_64 libcurl-7.87.0-4.fc38.x86_64 libdb-5.3.28-55.fc38.x86_64 libeconf-0.4.0-5.fc38.x86_64 libevent-2.1.12-8.fc38.x86_64 libfdisk-2.38.1-4.fc38.x86_64 libffi-3.4.4-2.fc38.x86_64 libgcc-13.0.1-0.2.fc38.x86_64 libgomp-13.0.1-0.2.fc38.x86_64 libidn2-2.3.4-2.fc38.x86_64 libmount-2.38.1-4.fc38.x86_64 libnghttp2-1.51.0-2.fc38.x86_64 libnsl2-2.0.0-5.fc38.x86_64 libpkgconf-1.8.0-5.fc38.x86_64 libpsl-0.21.2-2.fc38.x86_64 libpwquality-1.4.5-3.fc38.x86_64 libselinux-3.5-0.rc2.1.fc38.1.x86_64 libsemanage-3.5-0.rc2.1.fc38.1.x86_64 libsepol-3.5-0.rc2.1.fc38.1.x86_64 libsigsegv-2.14-4.fc38.x86_64 libsmartcols-2.38.1-4.fc38.x86_64 libssh-0.10.4-3.fc38.x86_64 libssh-config-0.10.4-3.fc38.noarch libstdc++-13.0.1-0.2.fc38.x86_64 libtasn1-4.19.0-2.fc38.x86_64 libtirpc-1.3.3-1.fc38.x86_64 libunistring1.0-1.0-1.fc38.x86_64 libutempter-1.2.1-8.fc38.x86_64 libuuid-2.38.1-4.fc38.x86_64 libverto-0.3.2-5.fc38.x86_64 libxcrypt-4.4.33-7.fc39.x86_64 libxml2-2.10.3-3.fc38.x86_64 libzstd-1.5.4-1.fc39.x86_64 lua-libs-5.4.4-8.fc38.x86_64 lua-srpm-macros-1-8.fc38.noarch lz4-libs-1.9.4-2.fc38.x86_64 mpfr-4.1.1-3.fc38.x86_64 ncurses-base-6.4-3.20230114.fc38.noarch ncurses-libs-6.4-3.20230114.fc38.x86_64 nettle-3.8-3.fc38.x86_64 nim-srpm-macros-3-8.fc38.noarch ocaml-srpm-macros-7-3.fc38.noarch openblas-srpm-macros-2-13.fc38.noarch openldap-2.6.3-2.fc38.x86_64 openssl-libs-1:3.0.8-1.fc39.x86_64 p11-kit-0.24.1-6.fc38.x86_64 p11-kit-trust-0.24.1-6.fc38.x86_64 package-notes-srpm-macros-0.5-7.fc38.noarch pam-1.5.2-16.fc38.x86_64 pam-libs-1.5.2-16.fc38.x86_64 patch-2.7.6-19.fc38.x86_64 pcre2-10.42-1.fc38.1.x86_64 pcre2-syntax-10.42-1.fc38.1.noarch perl-srpm-macros-1-48.fc38.noarch pkgconf-1.8.0-5.fc38.x86_64 pkgconf-m4-1.8.0-5.fc38.noarch pkgconf-pkg-config-1.8.0-5.fc38.x86_64 popt-1.19-2.fc38.x86_64 publicsuffix-list-dafsa-20221208-2.fc38.noarch pyproject-srpm-macros-1.6.2-1.fc39.noarch python-srpm-macros-3.11-9.fc38.noarch qt5-srpm-macros-5.15.8-2.fc38.noarch readline-8.2-3.fc38.x86_64 redhat-rpm-config-249-1.fc39.noarch rpm-4.18.0-10.fc38.x86_64 rpm-build-4.18.0-10.fc38.x86_64 rpm-build-libs-4.18.0-10.fc38.x86_64 rpm-libs-4.18.0-10.fc38.x86_64 rpm-sequoia-1.2.0-3.fc38.x86_64 rpmautospec-rpm-macros-0.3.5-1.fc38.noarch rust-srpm-macros-23-2.fc38.noarch sed-4.8-12.fc38.x86_64 setup-2.14.3-2.fc38.noarch shadow-utils-2:4.13-4.fc38.x86_64 sqlite-libs-3.40.1-2.fc38.x86_64 systemd-libs-253~rc3-1.fc39.x86_64 tar-2:1.34-7.fc38.x86_64 tzdata-2022g-2.fc38.noarch unzip-6.0-60.fc38.x86_64 util-linux-2.38.1-4.fc38.x86_64 util-linux-core-2.38.1-4.fc38.x86_64 which-2.21-37.fc38.x86_64 xxhash-libs-0.8.1-4.fc38.x86_64 xz-5.4.1-1.fc38.x86_64 xz-libs-5.4.1-1.fc38.x86_64 zip-3.0-36.fc38.x86_64 zlib-1.2.13-3.fc38.x86_64 zstd-1.5.4-1.fc39.x86_64 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: openblas-srpm-macros-2-13.fc38.noarch libarchive-3.6.1-5.fc39.x86_64 rpmautospec-rpm-macros-0.3.5-1.fc38.noarch libselinux-3.5-0.rc2.1.fc38.1.x86_64 lua-libs-5.4.4-8.fc38.x86_64 fedora-release-identity-basic-39-0.1.noarch fpc-srpm-macros-1.3-7.fc38.noarch util-linux-2.38.1-4.fc38.x86_64 ed-1.19-2.fc38.x86_64 libverto-0.3.2-5.fc38.x86_64 basesystem-11-15.fc38.noarch openssl-libs-3.0.8-1.fc39.x86_64 glibc-2.37-1.fc38.x86_64 openldap-2.6.3-2.fc38.x86_64 xz-libs-5.4.1-1.fc38.x86_64 elfutils-0.188-5.fc38.x86_64 python-srpm-macros-3.11-9.fc38.noarch ghc-srpm-macros-1.6.1-1.fc38.noarch libacl-2.3.1-6.fc38.x86_64 libuuid-2.38.1-4.fc38.x86_64 libcom_err-1.46.5-4.fc38.x86_64 libdb-5.3.28-55.fc38.x86_64 shadow-utils-4.13-4.fc38.x86_64 libpsl-0.21.2-2.fc38.x86_64 libeconf-0.4.0-5.fc38.x86_64 lua-srpm-macros-1-8.fc38.noarch file-libs-5.44-2.fc39.x86_64 sed-4.8-12.fc38.x86_64 p11-kit-0.24.1-6.fc38.x86_64 diffutils-3.9-1.fc38.x86_64 zlib-1.2.13-3.fc38.x86_64 patch-2.7.6-19.fc38.x86_64 nettle-3.8-3.fc38.x86_64 libstdc++-13.0.1-0.2.fc38.x86_64 keyutils-libs-1.6.1-6.fc38.x86_64 ncurses-base-6.4-3.20230114.fc38.noarch setup-2.14.3-2.fc38.noarch libgcc-13.0.1-0.2.fc38.x86_64 libpkgconf-1.8.0-5.fc38.x86_64 gdb-minimal-12.1-16.fc38.x86_64 xz-5.4.1-1.fc38.x86_64 libxcrypt-4.4.33-7.fc39.x86_64 publicsuffix-list-dafsa-20221208-2.fc38.noarch libmount-2.38.1-4.fc38.x86_64 fedora-repos-rawhide-39-0.1.noarch redhat-rpm-config-249-1.fc39.noarch file-5.44-2.fc39.x86_64 coreutils-9.1-11.fc38.x86_64 fedora-gpg-keys-39-0.1.noarch pam-1.5.2-16.fc38.x86_64 glibc-gconv-extra-2.37-1.fc38.x86_64 debugedit-5.0-7.fc38.x86_64 package-notes-srpm-macros-0.5-7.fc38.noarch gnat-srpm-macros-6-2.fc38.noarch binutils-gold-2.39-9.fc38.x86_64 fedora-release-common-39-0.1.noarch xxhash-libs-0.8.1-4.fc38.x86_64 cyrus-sasl-lib-2.1.28-9.fc38.x86_64 pyproject-srpm-macros-1.6.2-1.fc39.noarch tzdata-2022g-2.fc38.noarch binutils-2.39-9.fc38.x86_64 fedora-repos-39-0.1.noarch libunistring1.0-1.0-1.fc38.x86_64 popt-1.19-2.fc38.x86_64 rpm-build-libs-4.18.0-10.fc38.x86_64 glibc-common-2.37-1.fc38.x86_64 elfutils-libs-0.188-5.fc38.x86_64 pkgconf-1.8.0-5.fc38.x86_64 pkgconf-m4-1.8.0-5.fc38.noarch libssh-config-0.10.4-3.fc38.noarch rpm-build-4.18.0-10.fc38.x86_64 lz4-libs-1.9.4-2.fc38.x86_64 nim-srpm-macros-3-8.fc38.noarch libxml2-2.10.3-3.fc38.x86_64 elfutils-default-yama-scope-0.188-5.fc38.noarch gawk-5.1.1-5.fc38.x86_64 gzip-1.12-3.fc38.x86_64 pkgconf-pkg-config-1.8.0-5.fc38.x86_64 ca-certificates-2023.2.60-2.fc38.noarch libgomp-13.0.1-0.2.fc38.x86_64 libfdisk-2.38.1-4.fc38.x86_64 perl-srpm-macros-1-48.fc38.noarch libcurl-7.87.0-4.fc38.x86_64 qt5-srpm-macros-5.15.8-2.fc38.noarch libevent-2.1.12-8.fc38.x86_64 info-7.0.2-1.fc38.x86_64 crypto-policies-20221215-2.gita4c31a3.fc38.noarch libcap-ng-0.8.3-5.fc38.x86_64 bash-5.2.15-3.fc38.x86_64 kernel-srpm-macros-1.0-16.fc38.noarch which-2.21-37.fc38.x86_64 libsepol-3.5-0.rc2.1.fc38.1.x86_64 libtirpc-1.3.3-1.fc38.x86_64 pcre2-syntax-10.42-1.fc38.1.noarch cracklib-2.9.7-31.fc38.x86_64 libsigsegv-2.14-4.fc38.x86_64 elfutils-debuginfod-client-0.188-5.fc38.x86_64 rpm-4.18.0-10.fc38.x86_64 tar-1.34-7.fc38.x86_64 elfutils-libelf-0.188-5.fc38.x86_64 fedora-release-39-0.1.noarch bzip2-libs-1.0.8-13.fc38.x86_64 sqlite-libs-3.40.1-2.fc38.x86_64 libutempter-1.2.1-8.fc38.x86_64 gpg-pubkey-18b8e74c-62f2920f libbrotli-1.0.9-11.fc38.x86_64 cpio-2.13-14.fc38.x86_64 grep-3.8-3.fc38.x86_64 filesystem-3.18-3.fc38.x86_64 rust-srpm-macros-23-2.fc38.noarch coreutils-common-9.1-11.fc38.x86_64 fonts-srpm-macros-2.0.5-11.fc38.noarch libnghttp2-1.51.0-2.fc38.x86_64 jansson-2.13.1-6.fc38.x86_64 gmp-6.2.1-4.fc38.x86_64 libnsl2-2.0.0-5.fc38.x86_64 pam-libs-1.5.2-16.fc38.x86_64 bzip2-1.0.8-13.fc38.x86_64 glibc-minimal-langpack-2.37-1.fc38.x86_64 pcre2-10.42-1.fc38.1.x86_64 alternatives-1.21-2.fc38.x86_64 go-srpm-macros-3.2.0-2.fc38.noarch readline-8.2-3.fc38.x86_64 gdbm-libs-1.23-3.fc38.x86_64 libtasn1-4.19.0-2.fc38.x86_64 systemd-libs-253~rc3-1.fc39.x86_64 p11-kit-trust-0.24.1-6.fc38.x86_64 ansible-srpm-macros-1-9.1.fc38.noarch efi-srpm-macros-5-7.fc38.noarch authselect-libs-1.4.2-2.fc38.x86_64 zip-3.0-36.fc38.x86_64 libblkid-2.38.1-4.fc38.x86_64 curl-7.87.0-4.fc38.x86_64 rpm-sequoia-1.2.0-3.fc38.x86_64 authselect-1.4.2-2.fc38.x86_64 libssh-0.10.4-3.fc38.x86_64 ocaml-srpm-macros-7-3.fc38.noarch audit-libs-3.1-2.fc39.x86_64 zstd-1.5.4-1.fc39.x86_64 mpfr-4.1.1-3.fc38.x86_64 libsemanage-3.5-0.rc2.1.fc38.1.x86_64 libzstd-1.5.4-1.fc39.x86_64 libidn2-2.3.4-2.fc38.x86_64 rpm-libs-4.18.0-10.fc38.x86_64 krb5-libs-1.20.1-9.fc39.x86_64 findutils-4.9.0-3.fc38.x86_64 libpwquality-1.4.5-3.fc38.x86_64 libffi-3.4.4-2.fc38.x86_64 gpg-pubkey-eb10b464-6202d9c6 libattr-2.5.1-6.fc38.x86_64 unzip-6.0-60.fc38.x86_64 util-linux-core-2.38.1-4.fc38.x86_64 dwz-0.15-2.fc38.x86_64 libcap-2.48-6.fc38.x86_64 libsmartcols-2.38.1-4.fc38.x86_64 ncurses-libs-6.4-3.20230114.fc38.x86_64 Start: buildsrpm Start: rpmbuild -bs Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658275200 Wrote: /builddir/build/SRPMS/bowtie2-2.4.1-6.fc39.src.rpm Finish: rpmbuild -bs cp: ‘var/lib/mock/fedora-rawhide-x86_64-1676384685.626650/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1676384685.626650/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1676384685.626650/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1676384685.626650/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-j9g64gno/bowtie2/bowtie2.spec) Config(child) 2 minutes 11 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 (timeout=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/bowtie2-2.4.1-6.fc39.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1676384685.626650 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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/results/bowtie2-2.4.1-6.fc39.src.rpm) Config(fedora-rawhide-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1676384685.626650/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-x86_64-bootstrap-1676384685.626650/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-x86_64-1676384685.626650/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 12 kB/s | 3.0 kB 00:00 fedora 28 kB/s | 6.9 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for bowtie2-2.4.1-6.fc39.src.rpm Start: build setup for bowtie2-2.4.1-6.fc39.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658275200 Wrote: /builddir/build/SRPMS/bowtie2-2.4.1-6.fc39.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Copr repository 12 kB/s | 3.0 kB 00:00 fedora 28 kB/s | 6.9 kB 00:00 Dependencies resolved. ================================================================================ Package Arch Version Repository Size ================================================================================ Installing: gcc-c++ x86_64 13.0.1-0.2.fc38 fedora 13 M help2man noarch 1.49.3-2.fc38 fedora 228 k libasan x86_64 13.0.1-0.2.fc38 fedora 452 k libubsan x86_64 13.0.1-0.2.fc38 fedora 194 k make x86_64 1:4.4-3.fc38 fedora 580 k perl-Clone x86_64 0.46-2.fc38 fedora 22 k perl-File-Which noarch 1.27-7.fc38 fedora 22 k perl-FindBin noarch 1.53-495.fc38 fedora 16 k perl-Sys-Hostname x86_64 1.24-495.fc38 fedora 19 k perl-Test-Deep noarch 1.204-2.fc38 fedora 120 k perl-generators noarch 1.16-2.fc38 fedora 17 k perl-interpreter x86_64 4:5.36.0-495.fc38 fedora 74 k perl-lib x86_64 0.65-495.fc38 fedora 17 k python3 x86_64 3.11.2-1.fc39 fedora 28 k tbb-devel x86_64 2020.3-15.fc39 copr_base 314 k zlib-devel x86_64 1.2.13-3.fc38 fedora 45 k Installing dependencies: annobin-docs noarch 11.09-1.fc38 fedora 94 k annobin-plugin-gcc x86_64 11.09-1.fc38 fedora 892 k cmake-filesystem x86_64 3.26.0~rc2-1.fc39 fedora 17 k cpp x86_64 13.0.1-0.2.fc38 fedora 11 M expat x86_64 2.5.0-2.fc38 fedora 110 k gc x86_64 8.2.2-3.fc38 fedora 110 k gcc x86_64 13.0.1-0.2.fc38 fedora 34 M gcc-plugin-annobin x86_64 13.0.1-0.2.fc38 fedora 31 k glibc-devel x86_64 2.37-1.fc38 fedora 50 k glibc-headers-x86 noarch 2.37-1.fc38 fedora 530 k groff-base x86_64 1.22.4-11.fc38 fedora 1.1 M guile22 x86_64 2.2.7-7.fc38 fedora 6.5 M kernel-headers x86_64 6.2.0-0.rc8.git0.1.fc39 fedora 1.5 M libb2 x86_64 0.98.1-8.fc38 fedora 25 k libmpc x86_64 1.3.1-2.fc38 fedora 70 k libstdc++-devel x86_64 13.0.1-0.2.fc38 fedora 2.6 M libtool-ltdl x86_64 2.4.7-6.fc38 fedora 37 k libxcrypt-devel x86_64 4.4.33-7.fc39 fedora 30 k mpdecimal x86_64 2.5.1-6.fc38 fedora 89 k ncurses x86_64 6.4-3.20230114.fc38 fedora 412 k perl-AutoLoader noarch 5.74-495.fc38 fedora 23 k perl-B x86_64 1.83-495.fc38 fedora 184 k perl-Carp noarch 1.52-490.fc38 fedora 29 k perl-Class-Struct noarch 0.66-495.fc38 fedora 24 k perl-Data-Dumper x86_64 2.184-491.fc38 fedora 56 k perl-DynaLoader x86_64 1.52-495.fc38 fedora 28 k perl-Encode x86_64 4:3.19-493.fc38 fedora 1.7 M perl-Errno x86_64 1.36-495.fc38 fedora 17 k perl-Exporter noarch 5.77-490.fc38 fedora 31 k perl-Fcntl x86_64 1.15-495.fc38 fedora 23 k perl-Fedora-VSP noarch 0.001-31.fc38 fedora 23 k perl-File-Basename noarch 2.85-495.fc38 fedora 19 k perl-File-Path noarch 2.18-490.fc38 fedora 35 k perl-File-Temp noarch 1:0.231.100-490.fc38 fedora 59 k perl-File-stat noarch 1.12-495.fc38 fedora 19 k perl-Getopt-Long noarch 1:2.54-2.fc38 fedora 60 k perl-Getopt-Std noarch 1.13-495.fc38 fedora 18 k perl-HTTP-Tiny noarch 0.082-2.fc38 fedora 55 k perl-IO x86_64 1.50-495.fc38 fedora 94 k perl-IPC-Open3 noarch 1.22-495.fc38 fedora 25 k perl-Importer noarch 0.026-9.fc38 fedora 39 k perl-JSON-PP noarch 1:4.16-2.fc38 fedora 67 k perl-MIME-Base64 x86_64 3.16-490.fc38 fedora 30 k perl-Math-BigInt noarch 1:1.9998.37-3.fc38 fedora 204 k perl-Math-BigRat noarch 0.2624-3.fc38 fedora 41 k perl-Math-Complex noarch 1.59-495.fc38 fedora 49 k perl-Object-HashBase noarch 0.009-12.fc38 fedora 25 k perl-POSIX x86_64 2.03-495.fc38 fedora 100 k perl-PathTools x86_64 3.84-490.fc38 fedora 87 k perl-Pod-Escapes noarch 1:1.07-490.fc38 fedora 20 k perl-Pod-Perldoc noarch 3.28.01-491.fc38 fedora 86 k perl-Pod-Simple noarch 1:3.43-491.fc38 fedora 219 k perl-Pod-Usage noarch 4:2.03-4.fc38 fedora 40 k perl-Scalar-List-Utils x86_64 5:1.63-490.fc38 fedora 72 k perl-SelectSaver noarch 1.02-495.fc38 fedora 14 k perl-Socket x86_64 4:2.036-2.fc38 fedora 55 k perl-Storable x86_64 1:3.26-490.fc38 fedora 97 k perl-Symbol noarch 1.09-495.fc38 fedora 16 k perl-Term-ANSIColor noarch 5.01-491.fc38 fedora 47 k perl-Term-Cap noarch 1.18-1.fc39 fedora 22 k perl-Term-Table noarch 0.016-6.fc38 fedora 34 k perl-Test-Simple noarch 3:1.302192-1.fc38 fedora 574 k perl-Text-ParseWords noarch 3.31-490.fc38 fedora 16 k perl-Text-Tabs+Wrap noarch 2021.0814-490.fc38 fedora 22 k perl-Time-HiRes x86_64 4:1.9770-490.fc38 fedora 57 k perl-Time-Local noarch 2:1.300-490.fc38 fedora 33 k perl-base noarch 2.27-495.fc38 fedora 18 k perl-constant noarch 1.33-491.fc38 fedora 23 k perl-if noarch 0.61.000-495.fc38 fedora 16 k perl-libs x86_64 4:5.36.0-495.fc38 fedora 2.2 M perl-macros noarch 4:5.36.0-495.fc38 fedora 14 k perl-mro x86_64 1.26-495.fc38 fedora 31 k perl-overload noarch 1.35-495.fc38 fedora 48 k perl-overloading noarch 0.02-495.fc38 fedora 15 k perl-parent noarch 1:0.239-2.fc38 fedora 14 k perl-podlators noarch 1:5.01-2.fc38 fedora 125 k perl-vars noarch 1.05-495.fc38 fedora 15 k python-pip-wheel noarch 22.3.1-2.fc38 fedora 1.4 M python-setuptools-wheel noarch 65.5.1-2.fc38 fedora 715 k python3-libs x86_64 3.11.2-1.fc39 fedora 9.6 M tbb x86_64 2020.3-15.fc39 copr_base 170 k Transaction Summary ================================================================================ Install 97 Packages Total download size: 93 M Installed size: 309 M Downloading Packages: (1/97): tbb-2020.3-15.fc39.x86_64.rpm 1.8 MB/s | 170 kB 00:00 (2/97): tbb-devel-2020.3-15.fc39.x86_64.rpm 3.2 MB/s | 314 kB 00:00 (3/97): annobin-docs-11.09-1.fc38.noarch.rpm 891 kB/s | 94 kB 00:00 (4/97): cmake-filesystem-3.26.0~rc2-1.fc39.x86_ 379 kB/s | 17 kB 00:00 (5/97): expat-2.5.0-2.fc38.x86_64.rpm 2.0 MB/s | 110 kB 00:00 (6/97): annobin-plugin-gcc-11.09-1.fc38.x86_64. 4.2 MB/s | 892 kB 00:00 (7/97): cpp-13.0.1-0.2.fc38.x86_64.rpm 35 MB/s | 11 MB 00:00 (8/97): gc-8.2.2-3.fc38.x86_64.rpm 305 kB/s | 110 kB 00:00 (9/97): gcc-plugin-annobin-13.0.1-0.2.fc38.x86_ 1.1 MB/s | 31 kB 00:00 (10/97): glibc-devel-2.37-1.fc38.x86_64.rpm 977 kB/s | 50 kB 00:00 (11/97): gcc-c++-13.0.1-0.2.fc38.x86_64.rpm 40 MB/s | 13 MB 00:00 (12/97): groff-base-1.22.4-11.fc38.x86_64.rpm 30 MB/s | 1.1 MB 00:00 (13/97): glibc-headers-x86-2.37-1.fc38.noarch.r 3.6 MB/s | 530 kB 00:00 (14/97): help2man-1.49.3-2.fc38.noarch.rpm 1.9 MB/s | 228 kB 00:00 (15/97): guile22-2.2.7-7.fc38.x86_64.rpm 34 MB/s | 6.5 MB 00:00 (16/97): libasan-13.0.1-0.2.fc38.x86_64.rpm 7.0 MB/s | 452 kB 00:00 (17/97): libb2-0.98.1-8.fc38.x86_64.rpm 1.3 MB/s | 25 kB 00:00 (18/97): libmpc-1.3.1-2.fc38.x86_64.rpm 4.6 MB/s | 70 kB 00:00 (19/97): kernel-headers-6.2.0-0.rc8.git0.1.fc39 6.2 MB/s | 1.5 MB 00:00 (20/97): libstdc++-devel-13.0.1-0.2.fc38.x86_64 29 MB/s | 2.6 MB 00:00 (21/97): libtool-ltdl-2.4.7-6.fc38.x86_64.rpm 2.1 MB/s | 37 kB 00:00 (22/97): libubsan-13.0.1-0.2.fc38.x86_64.rpm 3.8 MB/s | 194 kB 00:00 (23/97): libxcrypt-devel-4.4.33-7.fc39.x86_64.r 760 kB/s | 30 kB 00:00 (24/97): mpdecimal-2.5.1-6.fc38.x86_64.rpm 3.2 MB/s | 89 kB 00:00 (25/97): make-4.4-3.fc38.x86_64.rpm 18 MB/s | 580 kB 00:00 (26/97): perl-AutoLoader-5.74-495.fc38.noarch.r 1.5 MB/s | 23 kB 00:00 (27/97): perl-B-1.83-495.fc38.x86_64.rpm 9.3 MB/s | 184 kB 00:00 (28/97): ncurses-6.4-3.20230114.fc38.x86_64.rpm 8.3 MB/s | 412 kB 00:00 (29/97): perl-Carp-1.52-490.fc38.noarch.rpm 1.6 MB/s | 29 kB 00:00 (30/97): perl-Class-Struct-0.66-495.fc38.noarch 1.3 MB/s | 24 kB 00:00 (31/97): perl-Clone-0.46-2.fc38.x86_64.rpm 478 kB/s | 22 kB 00:00 (32/97): perl-Data-Dumper-2.184-491.fc38.x86_64 1.4 MB/s | 56 kB 00:00 (33/97): perl-DynaLoader-1.52-495.fc38.x86_64.r 1.3 MB/s | 28 kB 00:00 (34/97): perl-Errno-1.36-495.fc38.x86_64.rpm 761 kB/s | 17 kB 00:00 (35/97): perl-Exporter-5.77-490.fc38.noarch.rpm 1.2 MB/s | 31 kB 00:00 (36/97): perl-Fcntl-1.15-495.fc38.x86_64.rpm 947 kB/s | 23 kB 00:00 (37/97): perl-Fedora-VSP-0.001-31.fc38.noarch.r 396 kB/s | 23 kB 00:00 (38/97): perl-Encode-3.19-493.fc38.x86_64.rpm 11 MB/s | 1.7 MB 00:00 (39/97): perl-File-Path-2.18-490.fc38.noarch.rp 1.6 MB/s | 35 kB 00:00 (40/97): perl-File-Temp-0.231.100-490.fc38.noar 3.1 MB/s | 59 kB 00:00 (41/97): perl-File-Which-1.27-7.fc38.noarch.rpm 1.3 MB/s | 22 kB 00:00 (42/97): gcc-13.0.1-0.2.fc38.x86_64.rpm 26 MB/s | 34 MB 00:01 (43/97): perl-File-Basename-2.85-495.fc38.noarc 169 kB/s | 19 kB 00:00 (44/97): perl-File-stat-1.12-495.fc38.noarch.rp 431 kB/s | 19 kB 00:00 (45/97): perl-Getopt-Long-2.54-2.fc38.noarch.rp 3.9 MB/s | 60 kB 00:00 (46/97): perl-Getopt-Std-1.13-495.fc38.noarch.r 1.1 MB/s | 18 kB 00:00 (47/97): perl-HTTP-Tiny-0.082-2.fc38.noarch.rpm 3.4 MB/s | 55 kB 00:00 (48/97): perl-IO-1.50-495.fc38.x86_64.rpm 4.5 MB/s | 94 kB 00:00 (49/97): perl-IPC-Open3-1.22-495.fc38.noarch.rp 1.7 MB/s | 25 kB 00:00 (50/97): perl-Importer-0.026-9.fc38.noarch.rpm 2.2 MB/s | 39 kB 00:00 (51/97): perl-JSON-PP-4.16-2.fc38.noarch.rpm 4.1 MB/s | 67 kB 00:00 (52/97): perl-FindBin-1.53-495.fc38.noarch.rpm 251 kB/s | 16 kB 00:00 (53/97): perl-MIME-Base64-3.16-490.fc38.x86_64. 1.9 MB/s | 30 kB 00:00 (54/97): perl-Math-BigInt-1.9998.37-3.fc38.noar 10 MB/s | 204 kB 00:00 (55/97): perl-Math-Complex-1.59-495.fc38.noarch 2.6 MB/s | 49 kB 00:00 (56/97): perl-Object-HashBase-0.009-12.fc38.noa 1.7 MB/s | 25 kB 00:00 (57/97): perl-POSIX-2.03-495.fc38.x86_64.rpm 4.8 MB/s | 100 kB 00:00 (58/97): perl-PathTools-3.84-490.fc38.x86_64.rp 5.4 MB/s | 87 kB 00:00 (59/97): perl-Pod-Escapes-1.07-490.fc38.noarch. 1.2 MB/s | 20 kB 00:00 (60/97): perl-Pod-Perldoc-3.28.01-491.fc38.noar 5.2 MB/s | 86 kB 00:00 (61/97): perl-Pod-Usage-2.03-4.fc38.noarch.rpm 2.5 MB/s | 40 kB 00:00 (62/97): perl-Pod-Simple-3.43-491.fc38.noarch.r 6.8 MB/s | 219 kB 00:00 (63/97): perl-Scalar-List-Utils-1.63-490.fc38.x 3.7 MB/s | 72 kB 00:00 (64/97): perl-SelectSaver-1.02-495.fc38.noarch. 629 kB/s | 14 kB 00:00 (65/97): perl-Socket-2.036-2.fc38.x86_64.rpm 2.3 MB/s | 55 kB 00:00 (66/97): perl-Math-BigRat-0.2624-3.fc38.noarch. 299 kB/s | 41 kB 00:00 (67/97): perl-Symbol-1.09-495.fc38.noarch.rpm 672 kB/s | 16 kB 00:00 (68/97): perl-Term-ANSIColor-5.01-491.fc38.noar 2.0 MB/s | 47 kB 00:00 (69/97): perl-Term-Cap-1.18-1.fc39.noarch.rpm 1.3 MB/s | 22 kB 00:00 (70/97): perl-Term-Table-0.016-6.fc38.noarch.rp 1.7 MB/s | 34 kB 00:00 (71/97): perl-Sys-Hostname-1.24-495.fc38.x86_64 233 kB/s | 19 kB 00:00 (72/97): perl-Test-Deep-1.204-2.fc38.noarch.rpm 7.0 MB/s | 120 kB 00:00 (73/97): perl-Text-ParseWords-3.31-490.fc38.noa 882 kB/s | 16 kB 00:00 (74/97): perl-Text-Tabs+Wrap-2021.0814-490.fc38 1.5 MB/s | 22 kB 00:00 (75/97): perl-Time-HiRes-1.9770-490.fc38.x86_64 3.5 MB/s | 57 kB 00:00 (76/97): perl-Time-Local-1.300-490.fc38.noarch. 2.2 MB/s | 33 kB 00:00 (77/97): perl-base-2.27-495.fc38.noarch.rpm 1.2 MB/s | 18 kB 00:00 (78/97): perl-constant-1.33-491.fc38.noarch.rpm 1.4 MB/s | 23 kB 00:00 (79/97): perl-generators-1.16-2.fc38.noarch.rpm 1.0 MB/s | 17 kB 00:00 (80/97): perl-if-0.61.000-495.fc38.noarch.rpm 897 kB/s | 16 kB 00:00 (81/97): perl-interpreter-5.36.0-495.fc38.x86_6 3.0 MB/s | 74 kB 00:00 (82/97): perl-Storable-3.26-490.fc38.x86_64.rpm 346 kB/s | 97 kB 00:00 (83/97): perl-lib-0.65-495.fc38.x86_64.rpm 787 kB/s | 17 kB 00:00 (84/97): perl-macros-5.36.0-495.fc38.noarch.rpm 631 kB/s | 14 kB 00:00 (85/97): perl-mro-1.26-495.fc38.x86_64.rpm 1.4 MB/s | 31 kB 00:00 (86/97): perl-overload-1.35-495.fc38.noarch.rpm 2.4 MB/s | 48 kB 00:00 (87/97): perl-overloading-0.02-495.fc38.noarch. 1.0 MB/s | 15 kB 00:00 (88/97): perl-parent-0.239-2.fc38.noarch.rpm 942 kB/s | 14 kB 00:00 (89/97): perl-podlators-5.01-2.fc38.noarch.rpm 7.0 MB/s | 125 kB 00:00 (90/97): perl-vars-1.05-495.fc38.noarch.rpm 1.0 MB/s | 15 kB 00:00 (91/97): python-pip-wheel-22.3.1-2.fc38.noarch. 21 MB/s | 1.4 MB 00:00 (92/97): python-setuptools-wheel-65.5.1-2.fc38. 15 MB/s | 715 kB 00:00 (93/97): python3-3.11.2-1.fc39.x86_64.rpm 1.2 MB/s | 28 kB 00:00 (94/97): perl-Test-Simple-1.302192-1.fc38.noarc 889 kB/s | 574 kB 00:00 (95/97): python3-libs-3.11.2-1.fc39.x86_64.rpm 40 MB/s | 9.6 MB 00:00 (96/97): zlib-devel-1.2.13-3.fc38.x86_64.rpm 978 kB/s | 45 kB 00:00 (97/97): perl-libs-5.36.0-495.fc38.x86_64.rpm 1.5 MB/s | 2.2 MB 00:01 -------------------------------------------------------------------------------- Total 24 MB/s | 93 MB 00:03 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Preparing : 1/1 Installing : libmpc-1.3.1-2.fc38.x86_64 1/97 Installing : cpp-13.0.1-0.2.fc38.x86_64 2/97 Installing : python-setuptools-wheel-65.5.1-2.fc38.noarch 3/97 Installing : python-pip-wheel-22.3.1-2.fc38.noarch 4/97 Installing : ncurses-6.4-3.20230114.fc38.x86_64 5/97 Installing : mpdecimal-2.5.1-6.fc38.x86_64 6/97 Installing : libtool-ltdl-2.4.7-6.fc38.x86_64 7/97 Installing : libstdc++-devel-13.0.1-0.2.fc38.x86_64 8/97 Installing : libb2-0.98.1-8.fc38.x86_64 9/97 Installing : kernel-headers-6.2.0-0.rc8.git0.1.fc39.x86_64 10/97 Running scriptlet: groff-base-1.22.4-11.fc38.x86_64 11/97 Installing : groff-base-1.22.4-11.fc38.x86_64 11/97 Running scriptlet: groff-base-1.22.4-11.fc38.x86_64 11/97 Installing : perl-Text-Tabs+Wrap-2021.0814-490.fc38.noarch 12/97 Installing : perl-if-0.61.000-495.fc38.noarch 13/97 Installing : perl-Time-Local-2:1.300-490.fc38.noarch 14/97 Installing : perl-File-Path-2.18-490.fc38.noarch 15/97 Installing : 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ncurses-6.4-3.20230114.fc38.x86_64 27/97 Verifying : perl-AutoLoader-5.74-495.fc38.noarch 28/97 Verifying : perl-B-1.83-495.fc38.x86_64 29/97 Verifying : perl-Carp-1.52-490.fc38.noarch 30/97 Verifying : perl-Class-Struct-0.66-495.fc38.noarch 31/97 Verifying : perl-Clone-0.46-2.fc38.x86_64 32/97 Verifying : perl-Data-Dumper-2.184-491.fc38.x86_64 33/97 Verifying : perl-DynaLoader-1.52-495.fc38.x86_64 34/97 Verifying : perl-Encode-4:3.19-493.fc38.x86_64 35/97 Verifying : perl-Errno-1.36-495.fc38.x86_64 36/97 Verifying : perl-Exporter-5.77-490.fc38.noarch 37/97 Verifying : perl-Fcntl-1.15-495.fc38.x86_64 38/97 Verifying : perl-Fedora-VSP-0.001-31.fc38.noarch 39/97 Verifying : perl-File-Basename-2.85-495.fc38.noarch 40/97 Verifying : perl-File-Path-2.18-490.fc38.noarch 41/97 Verifying : perl-File-Temp-1:0.231.100-490.fc38.noarch 42/97 Verifying : perl-File-Which-1.27-7.fc38.noarch 43/97 Verifying : perl-File-stat-1.12-495.fc38.noarch 44/97 Verifying : perl-FindBin-1.53-495.fc38.noarch 45/97 Verifying : perl-Getopt-Long-1:2.54-2.fc38.noarch 46/97 Verifying : perl-Getopt-Std-1.13-495.fc38.noarch 47/97 Verifying : perl-HTTP-Tiny-0.082-2.fc38.noarch 48/97 Verifying : perl-IO-1.50-495.fc38.x86_64 49/97 Verifying : perl-IPC-Open3-1.22-495.fc38.noarch 50/97 Verifying : perl-Importer-0.026-9.fc38.noarch 51/97 Verifying : perl-JSON-PP-1:4.16-2.fc38.noarch 52/97 Verifying : perl-MIME-Base64-3.16-490.fc38.x86_64 53/97 Verifying : perl-Math-BigInt-1:1.9998.37-3.fc38.noarch 54/97 Verifying : perl-Math-BigRat-0.2624-3.fc38.noarch 55/97 Verifying : perl-Math-Complex-1.59-495.fc38.noarch 56/97 Verifying : perl-Object-HashBase-0.009-12.fc38.noarch 57/97 Verifying : perl-POSIX-2.03-495.fc38.x86_64 58/97 Verifying : perl-PathTools-3.84-490.fc38.x86_64 59/97 Verifying : perl-Pod-Escapes-1:1.07-490.fc38.noarch 60/97 Verifying : perl-Pod-Perldoc-3.28.01-491.fc38.noarch 61/97 Verifying : perl-Pod-Simple-1:3.43-491.fc38.noarch 62/97 Verifying : perl-Pod-Usage-4:2.03-4.fc38.noarch 63/97 Verifying : perl-Scalar-List-Utils-5:1.63-490.fc38.x86_64 64/97 Verifying : perl-SelectSaver-1.02-495.fc38.noarch 65/97 Verifying : perl-Socket-4:2.036-2.fc38.x86_64 66/97 Verifying : perl-Storable-1:3.26-490.fc38.x86_64 67/97 Verifying : perl-Symbol-1.09-495.fc38.noarch 68/97 Verifying : perl-Sys-Hostname-1.24-495.fc38.x86_64 69/97 Verifying : perl-Term-ANSIColor-5.01-491.fc38.noarch 70/97 Verifying : perl-Term-Cap-1.18-1.fc39.noarch 71/97 Verifying : perl-Term-Table-0.016-6.fc38.noarch 72/97 Verifying : perl-Test-Deep-1.204-2.fc38.noarch 73/97 Verifying : perl-Test-Simple-3:1.302192-1.fc38.noarch 74/97 Verifying : perl-Text-ParseWords-3.31-490.fc38.noarch 75/97 Verifying : perl-Text-Tabs+Wrap-2021.0814-490.fc38.noarch 76/97 Verifying : perl-Time-HiRes-4:1.9770-490.fc38.x86_64 77/97 Verifying : perl-Time-Local-2:1.300-490.fc38.noarch 78/97 Verifying : perl-base-2.27-495.fc38.noarch 79/97 Verifying : perl-constant-1.33-491.fc38.noarch 80/97 Verifying : perl-generators-1.16-2.fc38.noarch 81/97 Verifying : perl-if-0.61.000-495.fc38.noarch 82/97 Verifying : perl-interpreter-4:5.36.0-495.fc38.x86_64 83/97 Verifying : perl-lib-0.65-495.fc38.x86_64 84/97 Verifying : perl-libs-4:5.36.0-495.fc38.x86_64 85/97 Verifying : perl-macros-4:5.36.0-495.fc38.noarch 86/97 Verifying : perl-mro-1.26-495.fc38.x86_64 87/97 Verifying : perl-overload-1.35-495.fc38.noarch 88/97 Verifying : perl-overloading-0.02-495.fc38.noarch 89/97 Verifying : perl-parent-1:0.239-2.fc38.noarch 90/97 Verifying : perl-podlators-1:5.01-2.fc38.noarch 91/97 Verifying : perl-vars-1.05-495.fc38.noarch 92/97 Verifying : python-pip-wheel-22.3.1-2.fc38.noarch 93/97 Verifying : python-setuptools-wheel-65.5.1-2.fc38.noarch 94/97 Verifying : python3-3.11.2-1.fc39.x86_64 95/97 Verifying : python3-libs-3.11.2-1.fc39.x86_64 96/97 Verifying : zlib-devel-1.2.13-3.fc38.x86_64 97/97 Installed: annobin-docs-11.09-1.fc38.noarch annobin-plugin-gcc-11.09-1.fc38.x86_64 cmake-filesystem-3.26.0~rc2-1.fc39.x86_64 cpp-13.0.1-0.2.fc38.x86_64 expat-2.5.0-2.fc38.x86_64 gc-8.2.2-3.fc38.x86_64 gcc-13.0.1-0.2.fc38.x86_64 gcc-c++-13.0.1-0.2.fc38.x86_64 gcc-plugin-annobin-13.0.1-0.2.fc38.x86_64 glibc-devel-2.37-1.fc38.x86_64 glibc-headers-x86-2.37-1.fc38.noarch groff-base-1.22.4-11.fc38.x86_64 guile22-2.2.7-7.fc38.x86_64 help2man-1.49.3-2.fc38.noarch kernel-headers-6.2.0-0.rc8.git0.1.fc39.x86_64 libasan-13.0.1-0.2.fc38.x86_64 libb2-0.98.1-8.fc38.x86_64 libmpc-1.3.1-2.fc38.x86_64 libstdc++-devel-13.0.1-0.2.fc38.x86_64 libtool-ltdl-2.4.7-6.fc38.x86_64 libubsan-13.0.1-0.2.fc38.x86_64 libxcrypt-devel-4.4.33-7.fc39.x86_64 make-1:4.4-3.fc38.x86_64 mpdecimal-2.5.1-6.fc38.x86_64 ncurses-6.4-3.20230114.fc38.x86_64 perl-AutoLoader-5.74-495.fc38.noarch perl-B-1.83-495.fc38.x86_64 perl-Carp-1.52-490.fc38.noarch perl-Class-Struct-0.66-495.fc38.noarch perl-Clone-0.46-2.fc38.x86_64 perl-Data-Dumper-2.184-491.fc38.x86_64 perl-DynaLoader-1.52-495.fc38.x86_64 perl-Encode-4:3.19-493.fc38.x86_64 perl-Errno-1.36-495.fc38.x86_64 perl-Exporter-5.77-490.fc38.noarch perl-Fcntl-1.15-495.fc38.x86_64 perl-Fedora-VSP-0.001-31.fc38.noarch perl-File-Basename-2.85-495.fc38.noarch perl-File-Path-2.18-490.fc38.noarch perl-File-Temp-1:0.231.100-490.fc38.noarch perl-File-Which-1.27-7.fc38.noarch perl-File-stat-1.12-495.fc38.noarch perl-FindBin-1.53-495.fc38.noarch perl-Getopt-Long-1:2.54-2.fc38.noarch perl-Getopt-Std-1.13-495.fc38.noarch perl-HTTP-Tiny-0.082-2.fc38.noarch perl-IO-1.50-495.fc38.x86_64 perl-IPC-Open3-1.22-495.fc38.noarch perl-Importer-0.026-9.fc38.noarch perl-JSON-PP-1:4.16-2.fc38.noarch perl-MIME-Base64-3.16-490.fc38.x86_64 perl-Math-BigInt-1:1.9998.37-3.fc38.noarch perl-Math-BigRat-0.2624-3.fc38.noarch perl-Math-Complex-1.59-495.fc38.noarch perl-Object-HashBase-0.009-12.fc38.noarch perl-POSIX-2.03-495.fc38.x86_64 perl-PathTools-3.84-490.fc38.x86_64 perl-Pod-Escapes-1:1.07-490.fc38.noarch perl-Pod-Perldoc-3.28.01-491.fc38.noarch perl-Pod-Simple-1:3.43-491.fc38.noarch perl-Pod-Usage-4:2.03-4.fc38.noarch perl-Scalar-List-Utils-5:1.63-490.fc38.x86_64 perl-SelectSaver-1.02-495.fc38.noarch perl-Socket-4:2.036-2.fc38.x86_64 perl-Storable-1:3.26-490.fc38.x86_64 perl-Symbol-1.09-495.fc38.noarch perl-Sys-Hostname-1.24-495.fc38.x86_64 perl-Term-ANSIColor-5.01-491.fc38.noarch perl-Term-Cap-1.18-1.fc39.noarch perl-Term-Table-0.016-6.fc38.noarch perl-Test-Deep-1.204-2.fc38.noarch perl-Test-Simple-3:1.302192-1.fc38.noarch perl-Text-ParseWords-3.31-490.fc38.noarch perl-Text-Tabs+Wrap-2021.0814-490.fc38.noarch perl-Time-HiRes-4:1.9770-490.fc38.x86_64 perl-Time-Local-2:1.300-490.fc38.noarch perl-base-2.27-495.fc38.noarch perl-constant-1.33-491.fc38.noarch perl-generators-1.16-2.fc38.noarch perl-if-0.61.000-495.fc38.noarch perl-interpreter-4:5.36.0-495.fc38.x86_64 perl-lib-0.65-495.fc38.x86_64 perl-libs-4:5.36.0-495.fc38.x86_64 perl-macros-4:5.36.0-495.fc38.noarch perl-mro-1.26-495.fc38.x86_64 perl-overload-1.35-495.fc38.noarch perl-overloading-0.02-495.fc38.noarch perl-parent-1:0.239-2.fc38.noarch perl-podlators-1:5.01-2.fc38.noarch perl-vars-1.05-495.fc38.noarch python-pip-wheel-22.3.1-2.fc38.noarch python-setuptools-wheel-65.5.1-2.fc38.noarch python3-3.11.2-1.fc39.x86_64 python3-libs-3.11.2-1.fc39.x86_64 tbb-2020.3-15.fc39.x86_64 tbb-devel-2020.3-15.fc39.x86_64 zlib-devel-1.2.13-3.fc38.x86_64 Complete! Finish: build setup for bowtie2-2.4.1-6.fc39.src.rpm Start: rpmbuild bowtie2-2.4.1-6.fc39.src.rpm Building target platforms: x86_64 Building for target x86_64 setting SOURCE_DATE_EPOCH=1658275200 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.A944Fu + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf bowtie2-2.4.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/v2.4.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd bowtie2-2.4.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/bowtie2-makefile-cxxflags.patch + /usr/bin/patch -s --fuzz=0 --no-backup-if-mismatch -f + 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.3y0PYJ + umask 022 + cd /builddir/build/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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -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 bowtie2-2.4.1 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -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_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,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 -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_build.cpp:28: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ blockwise_sa.h: In instantiation of 'KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString; TIndexOffU = unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]': bt2_idx.h:1084:33: required from 'void Ebwt::initFromVector(EList&, EList&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString; TIndexOffU = unsigned int; std::ofstream = std::basic_ofstream; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' bt2_idx.h:657:23: required from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]' bt2_build.cpp:458:7: required from 'void driver(const std::string&, EList >&, const std::string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]' bt2_build.cpp:646:28: required from here blockwise_sa.h:483:24: warning: 'KarkkainenBlockwiseSA >::_done' will be initialized after [-Wreorder] 483 | volatile bool *_done; /// is a block processed? | ^~~~~ blockwise_sa.h:477:29: warning: 'bool KarkkainenBlockwiseSA >::thread_group_started' [-Wreorder] 477 | bool thread_group_started; | ^~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:202:9: warning: when initialized here [-Wreorder] 202 | KarkkainenBlockwiseSA(const TStr& __text, | ^~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In instantiation of 'KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]': bt2_idx.h:1084:33: required from 'void Ebwt::initFromVector(EList&, EList&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = S2bDnaString; TIndexOffU = unsigned int; std::ofstream = std::basic_ofstream; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' bt2_idx.h:657:23: required from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]' bt2_build.cpp:458:7: required from 'void driver(const std::string&, EList >&, const std::string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string]' bt2_build.cpp:657:25: required from here blockwise_sa.h:483:24: warning: 'KarkkainenBlockwiseSA::_done' will be initialized after [-Wreorder] 483 | volatile bool *_done; /// is a block processed? | ^~~~~ blockwise_sa.h:477:29: warning: 'bool KarkkainenBlockwiseSA::thread_group_started' [-Wreorder] 477 | bool thread_group_started; | ^~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:202:9: warning: when initialized here [-Wreorder] 202 | KarkkainenBlockwiseSA(const TStr& __text, | ^~~~~~~~~~~~~~~~~~~~~ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from diff_sample.h:24, from diff_sample.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -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_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,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 -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_build.cpp:28: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ blockwise_sa.h: In instantiation of 'KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString; TIndexOffU = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]': bt2_idx.h:1084:33: required from 'void Ebwt::initFromVector(EList&, EList&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = SString; TIndexOffU = long unsigned int; std::ofstream = std::basic_ofstream; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' bt2_idx.h:657:23: required from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = SString; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]' bt2_build.cpp:458:7: required from 'void driver(const std::string&, EList >&, const std::string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]' bt2_build.cpp:646:28: required from here blockwise_sa.h:483:24: warning: 'KarkkainenBlockwiseSA >::_done' will be initialized after [-Wreorder] 483 | volatile bool *_done; /// is a block processed? | ^~~~~ blockwise_sa.h:477:29: warning: 'bool KarkkainenBlockwiseSA >::thread_group_started' [-Wreorder] 477 | bool thread_group_started; | ^~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:202:9: warning: when initialized here [-Wreorder] 202 | KarkkainenBlockwiseSA(const TStr& __text, | ^~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h: In instantiation of 'KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]': bt2_idx.h:1084:33: required from 'void Ebwt::initFromVector(EList&, EList&, TIndexOffU, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, std::ofstream*, std::ofstream*, int, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, uint32_t, bool) [with TStr = S2bDnaString; TIndexOffU = long unsigned int; std::ofstream = std::basic_ofstream; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]' bt2_idx.h:657:23: required from 'Ebwt::Ebwt(TStr, bool, int, int, int32_t, int32_t, int32_t, int, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, TIndexOffU, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool, bool, bool) [with TStr = S2bDnaString; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]' bt2_build.cpp:458:7: required from 'void driver(const std::string&, EList >&, const std::string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string]' bt2_build.cpp:657:25: required from here blockwise_sa.h:483:24: warning: 'KarkkainenBlockwiseSA::_done' will be initialized after [-Wreorder] 483 | volatile bool *_done; /// is a block processed? | ^~~~~ blockwise_sa.h:477:29: warning: 'bool KarkkainenBlockwiseSA::thread_group_started' [-Wreorder] 477 | bool thread_group_started; | ^~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:202:9: warning: when initialized here [-Wreorder] 202 | KarkkainenBlockwiseSA(const TStr& __text, | ^~~~~~~~~~~~~~~~~~~~~ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from diff_sample.h:24, from diff_sample.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -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_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,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 -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_search.cpp:40: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:31, from blockwise_sa.h:35: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:25: required from here ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from bt2_search.cpp:21: /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair' declared here 187 | struct pair | ^~~~ In member function 'std::basic_ostream >::operator<<(void const*)', inlined from 'read_dir(char const*, int*)' at bt2_search.cpp:4610:53, inlined from 'steal_threads(int, int, EList&, EList&)void' at bt2_search.cpp:4626:27, inlined from 'thread_monitor(int, int, EList&, EList&)void' at bt2_search.cpp:4647:16, inlined from 'multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)' at bt2_search.cpp:4782:18: /usr/include/c++/13/ostream:293:25: warning: pointer may be used after 'closedir' [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function 'read_dir(char const*, int*)', inlined from 'steal_threads(int, int, EList&, EList&)void' at bt2_search.cpp:4626:27, inlined from 'thread_monitor(int, int, EList&, EList&)void' at bt2_search.cpp:4647:16, inlined from 'multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)' at bt2_search.cpp:4782:18: bt2_search.cpp:4608:20: note: call to 'closedir' here 4608 | if(closedir(dir) != 0) { | ~~~~~~~~^~~~~ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed.cpp:23: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_seed2.cpp:22: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from random_util.h:25, from aligner_seed2.h:101: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:25: required from here ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/utility:69, from aligner_seed2.h:98: /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair' declared here 187 | struct pair | ^~~~ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from random_util.h:25, from aligner_seed2.h:101: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:25: required from here ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/utility:69, from aligner_seed2.h:98: /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair' declared here 187 | struct pair | ^~~~ 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++/13/new: In function 'parseFasta': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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++/13/new: In function 'parseFasta': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In member function 'alloc', inlined from '_ZN5EListI14EIvalMergeListLi128EE15expandCopyExactEm.part.0' at ds.h:967:17: 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++/13/new: In member function '_ZN5EListI14EIvalMergeListLi128EE15expandCopyExactEm.part.0': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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:564:15, inlined from 'patsrcFromStrings' at pat.cpp:100:57: 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++/13/new: In function 'patsrcFromStrings': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In member function 'alloc', inlined from '_ZN5EListI11GroupWalk2SI10PListSliceImLi16384EELi16EELi128EE15expandCopyExactEm.part.0' at ds.h:967:17: 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++/13/new: In member function '_ZN5EListI11GroupWalk2SI10PListSliceImLi16384EELi16EELi128EE15expandCopyExactEm.part.0': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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 'push_back' at ds.h:496:29, inlined from 'setupPatternComposer.constprop' at pat.cpp:363:20: 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++/13/new: In function 'setupPatternComposer.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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:4923:14: 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++/13/new: In function 'driver.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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:434:15: 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++/13/new: In member function 'instantiateSeeds.isra': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -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_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,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 -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_search.cpp:40: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:31, from blockwise_sa.h:35: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:25: required from here ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /usr/include/c++/13/bits/locale_classes.h:40, from /usr/include/c++/13/bits/ios_base.h:41, from /usr/include/c++/13/ios:44, from /usr/include/c++/13/ostream:40, from /usr/include/c++/13/iostream:41, from bt2_search.cpp:21: /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair' declared here 187 | struct pair | ^~~~ In member function 'std::basic_ostream >::operator<<(void const*)', inlined from 'read_dir(char const*, int*)' at bt2_search.cpp:4610:53, inlined from 'steal_threads(int, int, EList&, EList&)void' at bt2_search.cpp:4626:27, inlined from 'thread_monitor(int, int, EList&, EList&)void' at bt2_search.cpp:4647:16, inlined from 'multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)' at bt2_search.cpp:4782:18: /usr/include/c++/13/ostream:293:25: warning: pointer may be used after 'closedir' [-Wuse-after-free] 293 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function 'read_dir(char const*, int*)', inlined from 'steal_threads(int, int, EList&, EList&)void' at bt2_search.cpp:4626:27, inlined from 'thread_monitor(int, int, EList&, EList&)void' at bt2_search.cpp:4647:16, inlined from 'multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)' at bt2_search.cpp:4782:18: bt2_search.cpp:4608:20: note: call to 'closedir' here 4608 | if(closedir(dir) != 0) { | ~~~~~~~~^~~~~ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed.cpp:23: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_seed2.cpp:22: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from random_util.h:25, from aligner_seed2.h:101: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:25: required from here ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/utility:69, from aligner_seed2.h:98: /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair' declared here 187 | struct pair | ^~~~ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from group_walk.h:86, from aligner_sw_driver.h:84, from aligner_sw_driver.cpp:47: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from aligner_seed2.h:103, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from random_util.h:25, from aligner_seed2.h:101: ds.h: In instantiation of 'EMap& EMap::operator=(const EMap&) [with K = DescentRedundancyKey; V = long int]': ds.h:973:12: required from 'void EList::expandCopyExact(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:958:3: required from 'void EList::expandCopy(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' ds.h:569:4: required from 'void EList::resize(size_t) [with T = EMap; int S = 8; size_t = long unsigned int]' aligner_seed2.h:482:25: required from here ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/utility:69, from aligner_seed2.h:98: /usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair' declared here 187 | struct pair | ^~~~ 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++/13/new: In function 'parseFasta': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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++/13/new: In function 'parseFasta': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In member function 'alloc', inlined from '_ZN5EListI14EIvalMergeListLi128EE15expandCopyExactEm.part.0' at ds.h:967:17: 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++/13/new: In member function '_ZN5EListI14EIvalMergeListLi128EE15expandCopyExactEm.part.0': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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:564:15, inlined from 'patsrcFromStrings' at pat.cpp:100:57: 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++/13/new: In function 'patsrcFromStrings': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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' at aligner_driver.cpp:317:16, inlined from 'multiseedSearchWorker_2p5' at bt2_search.cpp:4435:11: 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++/13/new: In function 'multiseedSearchWorker_2p5': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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' at aligner_driver.cpp:326:29, inlined from 'multiseedSearchWorker_2p5' at bt2_search.cpp:4435:11: 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++/13/new: In function 'multiseedSearchWorker_2p5': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In member function 'alloc', inlined from '_ZN5EListI10Random1toNLi16EE15expandCopyExactEm.part.0' at ds.h:967:17: 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++/13/new: In member function '_ZN5EListI10Random1toNLi16EE15expandCopyExactEm.part.0': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc) | ^ In member function 'alloc', inlined from '_ZN5EListI11GroupWalk2SI10PListSliceIjLi16384EELi16EELi128EE15expandCopyExactEm.part.0' at ds.h:967:17: 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++/13/new: In member function '_ZN5EListI11GroupWalk2SI10PListSliceIjLi16384EELi16EELi128EE15expandCopyExactEm.part.0': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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 'push_back' at ds.h:496:29, inlined from 'setupPatternComposer.constprop' at pat.cpp:363:20: 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++/13/new: In function 'setupPatternComposer.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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:4923:14: 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++/13/new: In function 'driver.constprop': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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:434:15: 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++/13/new: In member function 'instantiateSeeds.isra': /usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here 128 | _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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -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 -I . \ -o bowtie2-inspect-l bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.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,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 -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_inspect.cpp:29: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -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 -I . \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.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,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 -lz -lpthread -ltbb -ltbbmalloc_proxy In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_inspect.cpp:29: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_idx.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_io.cpp:25: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from blockwise_sa.h:24, from bt2_idx.h:42, from bt2_util.cpp:26: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ In file included from diff_sample.h:24, from multikey_qsort.h:27, from multikey_qsort.cpp:20: /usr/include/tbb/tbb.h:21:154: note: '#pragma message: TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.' 21 | #pragma message("TBB Warning: tbb.h contains deprecated functionality. For details, please see Deprecated Features appendix in the TBB reference manual.") | ^ + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.RRKosr + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64 ++ dirname /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64 + 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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -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 bowtie2-2.4.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64 'INSTALL=/usr/bin/install -p' PREFIX=/usr mkdir -p /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/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/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin ; \ done + mkdir -p /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/man/man1 + for cmd in bowtie2 bowtie2-{build,inspect} + help2man -N -s 1 -o /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/man/man1/bowtie2.1 --version-string=2.4.1 /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin/bowtie2 + for cmd in bowtie2 bowtie2-{build,inspect} + help2man -N -s 1 -o /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/man/man1/bowtie2-build.1 --version-string=2.4.1 /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin/bowtie2-build + for cmd in bowtie2 bowtie2-{build,inspect} + help2man -N -s 1 -o /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/man/man1/bowtie2-inspect.1 --version-string=2.4.1 /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin/bowtie2-inspect + /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 2.4.1-6.fc39 --unique-debug-suffix -2.4.1-6.fc39.x86_64 --unique-debug-src-base bowtie2-2.4.1-6.fc39.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/bowtie2-2.4.1 extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin/bowtie2-align-s extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin/bowtie2-align-l extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin/bowtie2-build-l extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin/bowtie2-build-s extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin/bowtie2-inspect-l extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/bin/bowtie2-inspect-s original debug info size: 26904kB, size after compression: 17936kB /usr/bin/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match. 4910 blocks + /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 Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.5eUUfm + umask 022 + cd /builddir/build/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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -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 -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 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -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 bowtie2-2.4.1 + for cmd in bowtie2 bowtie2-{build,inspect} + ./bowtie2 --version + grep 'version 2.4.1' /builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s version 2.4.1 + for cmd in bowtie2 bowtie2-{build,inspect} + ./bowtie2-build --version + grep 'version 2.4.1' /builddir/build/BUILD/bowtie2-2.4.1/bowtie2-build-s version 2.4.1 + for cmd in bowtie2 bowtie2-{build,inspect} + grep 'version 2.4.1' + ./bowtie2-inspect --version /builddir/build/BUILD/bowtie2-2.4.1/bowtie2-inspect-s version 2.4.1 + 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 4671. \1 better written as $1 at scripts/test/simple_tests.pl line 4672. 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 11 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 11 -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 3 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 3 -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 14 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 14 -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 4 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 4 -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 7 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:12 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --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 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.0 SO:unsorted @SQ SN:1 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -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:1.0 SO:unsorted @SQ SN:2 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.0 SO:unsorted @SQ SN:0 LN:34 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -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 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 5 -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 2 -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 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 3 -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 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 6 -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 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 13 -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 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: trim position must be either 3 or 5 Bowtie 2 version 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] Index filename prefix (minus trailing .X.bt2). NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. Files with #1 mates, paired with files in . Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with #2 mates, paired with files in . Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with unpaired reads. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with interleaved paired-end FASTQ/FASTA reads Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files are unaligned BAM sorted by read name. File for SAM output (default: stdout) , , 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:,i: query input files are continuous FASTA where reads are substrings (k-mers) extracted from a FASTA file and aligned at offsets 1, 1+i, 1+2i ... end of reference -c , , are sequences themselves, not files -s/--skip skip the first reads/pairs in the input (none) -u/--upto stop after first reads/pairs (no limit) -5/--trim5 trim bases from 5'/left end of reads (0) -3/--trim3 trim bases from 3'/right end of reads (0) --trim-to [3:|5:] trim reads exceeding 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 max # mismatches in seed alignment; can be 0 or 1 (0) -L length of seed substrings; must be >3, <32 (22) -i interval between seed substrings w/r/t read len (S,1,1.15) --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) --dpad include extra ref chars on sides of DP table (15) --gbar disallow gaps within 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 match bonus (0 for --end-to-end, 2 for --local) --mp max penalty for mismatch; lower qual = lower penalty (6) --np penalty for non-A/C/G/Ts in read/ref (1) --rdg , read gap open, extend penalties (5,3) --rfg , reference gap open, extend penalties (5,3) --score-min 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 report up to alns per read; MAPQ not meaningful OR -a/--all report all alignments; very slow, MAPQ not meaningful Effort: -D give up extending after failed extends in a row (15) -R for reads w/ repetitive seeds, try sets of seeds (2) Paired-end: -I/--minins minimum fragment length (0) -X/--maxins 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 write unpaired reads that didn't align to --al write unpaired reads that aligned at least once to --un-conc write pairs that didn't align concordantly to --al-conc write pairs that aligned concordantly at least once to (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) --quiet print nothing to stderr except serious errors --met-file send metrics to file at (off) --met-stderr send metrics to stderr (off) --met report internal counters & metrics every 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 set read group id, reflected in @RG line and RG:Z: opt field --rg add ("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 Performance: -p/--threads 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 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/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 6 -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 --trim-to 5:-12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: the number bases to trim must be at least 0 Bowtie 2 version 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] Index filename prefix (minus trailing .X.bt2). NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. Files with #1 mates, paired with files in . Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with #2 mates, paired with files in . Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with unpaired reads. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with interleaved paired-end FASTQ/FASTA reads Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files are unaligned BAM sorted by read name. File for SAM output (default: stdout) , , 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:,i: query input files are continuous FASTA where reads are substrings (k-mers) extracted from a FASTA file and aligned at offsets 1, 1+i, 1+2i ... end of reference -c , , are sequences themselves, not files -s/--skip skip the first reads/pairs in the input (none) -u/--upto stop after first reads/pairs (no limit) -5/--trim5 trim bases from 5'/left end of reads (0) -3/--trim3 trim bases from 3'/right end of reads (0) --trim-to [3:|5:] trim reads exceeding 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 max # mismatches in seed alignment; can be 0 or 1 (0) -L length of seed substrings; must be >3, <32 (22) -i interval between seed substrings w/r/t read len (S,1,1.15) --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) --dpad include extra ref chars on sides of DP table (15) --gbar disallow gaps within 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 match bonus (0 for --end-to-end, 2 for --local) --mp max penalty for mismatch; lower qual = lower penalty (6) --np penalty for non-A/C/G/Ts in read/ref (1) --rdg , read gap open, extend penalties (5,3) --rfg , reference gap open, extend penalties (5,3) --score-min 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 report up to alns per read; MAPQ not meaningful OR -a/--all report all alignments; very slow, MAPQ not meaningful Effort: -D give up extending after failed extends in a row (15) -R for reads w/ repetitive seeds, try sets of seeds (2) Paired-end: -I/--minins minimum fragment length (0) -X/--maxins 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 write unpaired reads that didn't align to --al write unpaired reads that aligned at least once to --un-conc write pairs that didn't align concordantly to --al-conc write pairs that aligned concordantly at least once to (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) --quiet print nothing to stderr except serious errors --met-file send metrics to file at (off) --met-stderr send metrics to stderr (off) --met report internal counters & metrics every 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 set read group id, reflected in @RG line and RG:Z: opt field --rg add ("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 Performance: -p/--threads 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 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/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 11 -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 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -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 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 11 -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 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" Cline multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -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 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -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 4 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 4 -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 7 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 14 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 2 -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 12 -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 12 -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 10 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -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 1 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 1 -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 8 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -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 13 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 10 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --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 multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -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 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 16 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -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 10 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 16 -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 12 -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 14 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 14 -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 3 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 3 -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 12 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -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 9 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --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 multiread 3 (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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -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 12 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 12 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -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 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -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 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 13 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 3 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 3 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 13 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 13 -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 13 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 13 -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 11 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -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 15 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 8 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -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 1 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -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 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 11 -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 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -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 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 14 -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 13 -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 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -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 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 7 -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 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -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 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -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 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -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 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -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 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --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 Tabbed paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA ./bowtie2 -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 13 -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 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 5049. Qseq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 5049. Qseq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -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 5049. Qseq 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 9 -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 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -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 5049. Qseq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --trim3 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 14 -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 5049. Qseq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -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 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --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 Qseq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -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 14 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 14 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 14 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 8 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 9 -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:1.0 SO:unsorted @SQ SN:0 LN:1192 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1028 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 = 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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:250 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:290 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 6 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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:-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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 14 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 13 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 12 -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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 7 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 3 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 4 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 4 -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 10 -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:1.0 SO:unsorted @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --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 -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 7 -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:1.0 SO:unsorted @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -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 11 -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:1.0 SO:unsorted @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 11 -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 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:1.0 SO:unsorted @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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" 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --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-discordant (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --ff --quiet -M 1 --no-discordant --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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 3 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --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-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 8 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-overlap --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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 9 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-contain --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-contain --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-overlap (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --no-overlap --ff --quiet -M 1 --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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:105 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:105 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --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:-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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 12 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 7 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 10 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 3 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --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:-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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:68 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:68 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -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 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:1.0 SO:unsorted @SQ SN:0 LN:528 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 9 -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 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:1.0 SO:unsorted @SQ SN:0 LN:528 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 11 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 10 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 13 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 10 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 15 -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 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:1.0 SO:unsorted @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --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 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:1.0 SO:unsorted @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 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 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 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:1.0 SO:unsorted @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 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 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 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:1.0 SO:unsorted @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 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 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 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:1.0 SO:unsorted @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 13 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 2 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 9 -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:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 16 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 6 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 13 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 10 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 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:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:120 @SQ SN:1 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 6 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:120 @SQ SN:1 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 10 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 8 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 1 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:47 @SQ SN:1 LN:27 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:47 @SQ SN:1 LN:27 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 11 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:61 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 2 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:61 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 3 -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:1.0 SO:unsorted @SQ SN:0 LN:23 @SQ SN:1 LN:28 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:23 @SQ SN:1 LN:28 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -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 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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --fr --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" 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 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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 7 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 3 -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 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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 2 --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" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 2 --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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 2 --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" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 4 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 12 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 9 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 13 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:3 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:3 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 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 --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 @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 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 (fw:1, sam:1) References: >0 TTGTTCGT ./bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --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 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 7 -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 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 @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 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" 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 8 -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:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 8 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 14 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 (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 @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --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 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --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 0 790 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --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 = 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 3 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 1 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --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 0 553 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 2 -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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 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 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -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 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 3 -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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 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 13 255 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 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 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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 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 79 255 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 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:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 -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:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:2607 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 16 -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 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:1.0 SO:unsorted @SQ SN:0 LN:2607 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 4 -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 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:1.0 SO:unsorted @SQ SN:0 LN:1906 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:1906 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -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 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 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:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -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:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 16 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 10 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 4 -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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 3 -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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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.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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 5 -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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 2 -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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 8 -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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 4 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --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 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 12 -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:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 1 -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 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:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 16 -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 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:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 8 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 14 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 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: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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 6 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 8 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 6 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 14 -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 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,.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:1.0 SO:unsorted @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --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,.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 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:1.0 SO:unsorted @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 16 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 4 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 4 -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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 5 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 14 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 8 -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:1.0 SO:unsorted @SQ SN:0 LN:18 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:18 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 --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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 3 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 2 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 11 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 13 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 5 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 (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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 13 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 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 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 5 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:25 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 7 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:25 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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: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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 2 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:10 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:10 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 3 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:22 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 16 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:22 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 12 -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 9 -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:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --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,.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 13 -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:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 13 -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 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:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --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" 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 7 -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:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 7 -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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 -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:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 -I 28 -X 80 --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:1.0 SO:unsorted @SQ SN:0 LN:41 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --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 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:41 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 8 -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 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:1.0 SO:unsorted @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --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 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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --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 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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --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 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --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 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 8 -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:1.0 SO:unsorted @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -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 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:1.0 SO:unsorted @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 15 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 8 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 1 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --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=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 7 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 14 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 5 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 5 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 14 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 14 -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 12 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 12 -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:1.0 SO:unsorted @SQ SN:0 LN:12 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.0 SO:unsorted @SQ SN:1 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -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 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.0 SO:unsorted @SQ SN:2 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.0 SO:unsorted @SQ SN:0 LN:34 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -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 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index --quiet -a --reads-per-batch 9 -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 11 -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 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 3 -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 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --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 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 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 7 -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 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: trim position must be either 3 or 5 Bowtie 2 version 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] Index filename prefix (minus trailing .X.bt2l). NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. Files with #1 mates, paired with files in . Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with #2 mates, paired with files in . Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with unpaired reads. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with interleaved paired-end FASTQ/FASTA reads Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files are unaligned BAM sorted by read name. File for SAM output (default: stdout) , , 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:,i: query input files are continuous FASTA where reads are substrings (k-mers) extracted from a FASTA file and aligned at offsets 1, 1+i, 1+2i ... end of reference -c , , are sequences themselves, not files -s/--skip skip the first reads/pairs in the input (none) -u/--upto stop after first reads/pairs (no limit) -5/--trim5 trim bases from 5'/left end of reads (0) -3/--trim3 trim bases from 3'/right end of reads (0) --trim-to [3:|5:] trim reads exceeding 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 max # mismatches in seed alignment; can be 0 or 1 (0) -L length of seed substrings; must be >3, <32 (22) -i interval between seed substrings w/r/t read len (S,1,1.15) --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) --dpad include extra ref chars on sides of DP table (15) --gbar disallow gaps within 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 match bonus (0 for --end-to-end, 2 for --local) --mp max penalty for mismatch; lower qual = lower penalty (6) --np penalty for non-A/C/G/Ts in read/ref (1) --rdg , read gap open, extend penalties (5,3) --rfg , reference gap open, extend penalties (5,3) --score-min 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 report up to alns per read; MAPQ not meaningful OR -a/--all report all alignments; very slow, MAPQ not meaningful Effort: -D give up extending after failed extends in a row (15) -R for reads w/ repetitive seeds, try sets of seeds (2) Paired-end: -I/--minins minimum fragment length (0) -X/--maxins 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 write unpaired reads that didn't align to --al write unpaired reads that aligned at least once to --un-conc write pairs that didn't align concordantly to --al-conc write pairs that aligned concordantly at least once to (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) --quiet print nothing to stderr except serious errors --met-file send metrics to file at (off) --met-stderr send metrics to stderr (off) --met report internal counters & metrics every 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 set read group id, reflected in @RG line and RG:Z: opt field --rg add ("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 Performance: -p/--threads 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 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/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII trim-to: invalid count (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 16 -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 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2 [options]* -x {-1 -2 | -U | --interleaved | -b } [-S ] Index filename prefix (minus trailing .X.bt2l). NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible. Files with #1 mates, paired with files in . Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with #2 mates, paired with files in . Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with unpaired reads. Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files with interleaved paired-end FASTQ/FASTA reads Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2). Files are unaligned BAM sorted by read name. File for SAM output (default: stdout) , , 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:,i: query input files are continuous FASTA where reads are substrings (k-mers) extracted from a FASTA file and aligned at offsets 1, 1+i, 1+2i ... end of reference -c , , are sequences themselves, not files -s/--skip skip the first reads/pairs in the input (none) -u/--upto stop after first reads/pairs (no limit) -5/--trim5 trim bases from 5'/left end of reads (0) -3/--trim3 trim bases from 3'/right end of reads (0) --trim-to [3:|5:] trim reads exceeding 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 max # mismatches in seed alignment; can be 0 or 1 (0) -L length of seed substrings; must be >3, <32 (22) -i interval between seed substrings w/r/t read len (S,1,1.15) --n-ceil func for max # non-A/C/G/Ts permitted in aln (L,0,0.15) --dpad include extra ref chars on sides of DP table (15) --gbar disallow gaps within 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 match bonus (0 for --end-to-end, 2 for --local) --mp max penalty for mismatch; lower qual = lower penalty (6) --np penalty for non-A/C/G/Ts in read/ref (1) --rdg , read gap open, extend penalties (5,3) --rfg , reference gap open, extend penalties (5,3) --score-min 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 report up to alns per read; MAPQ not meaningful OR -a/--all report all alignments; very slow, MAPQ not meaningful Effort: -D give up extending after failed extends in a row (15) -R for reads w/ repetitive seeds, try sets of seeds (2) Paired-end: -I/--minins minimum fragment length (0) -X/--maxins 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 write unpaired reads that didn't align to --al write unpaired reads that aligned at least once to --un-conc write pairs that didn't align concordantly to --al-conc write pairs that aligned concordantly at least once to (Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g. --un-gz , to gzip compress output, or add '-bz2' to bzip2 compress output.) --quiet print nothing to stderr except serious errors --met-file send metrics to file at (off) --met-stderr send metrics to stderr (off) --met report internal counters & metrics every 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 set read group id, reflected in @RG line and RG:Z: opt field --rg add ("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 Performance: -p/--threads 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 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/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 16 -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 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 4 -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 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 4 -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 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -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 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -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 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -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 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -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 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -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 1 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 1 -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 2 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -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 7 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -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 5 -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 13 -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 --large-index --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 --large-index --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index --trim5 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 10 -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 13 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -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 14 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 11 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --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 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 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 5 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 Fasta 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 Fasta 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --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 --large-index --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 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 15 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -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 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --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 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 6 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --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 multiline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -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 6 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --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 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 11 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 4 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -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 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 16 -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 14 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 3 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 14 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 13 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 13 -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 7 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 7 -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 14 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -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 11 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -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 8 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --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 Raw multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --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 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 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -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 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -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 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 Tabbed 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 13 -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 8 -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 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 13 -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 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 1 -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 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -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 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --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 multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -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 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -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 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -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 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -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 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 8 -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 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -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 5049. Qseq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -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 5049. Qseq 3 (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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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_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 5049. Qseq 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 6 -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 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -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 5049. Qseq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 4 -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 5049. Qseq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -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 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 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 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --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 Qseq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -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 12 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 8 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 9 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 2 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 7 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1192 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 15 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1028 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 = 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:250 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 15 -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:1.0 SO:unsorted @SQ SN:0 LN:290 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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^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:1.0 SO:unsorted @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:1.0 SO:unsorted @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:-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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 13 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 10 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 14 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 3 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 12 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 8 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 4 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 6 -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 11 -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:1.0 SO:unsorted @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 11 -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 13 -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:1.0 SO:unsorted @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -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 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:1.0 SO:unsorted @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 10 -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:1.0 SO:unsorted @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --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 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 11 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --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-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --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; --no-dovetail (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --no-dovetail --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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 11 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 3 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-overlap --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" 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 5 -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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index --no-contain --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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-contain --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-overlap (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --no-overlap --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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-overlap --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" 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:1.0 SO:unsorted @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:1.0 SO:unsorted @SQ SN:0 LN:105 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:105 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --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:-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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 4 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 7 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 11 -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 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:1.0 SO:unsorted @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index -L 6 --mp 6,3 --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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --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:-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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --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:-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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:68 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:68 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -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 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:1.0 SO:unsorted @SQ SN:0 LN:528 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -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 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:1.0 SO:unsorted @SQ SN:0 LN:528 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 0 289 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 12 -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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 14 -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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 4 -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 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:1.0 SO:unsorted @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 10 -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 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:1.0 SO:unsorted @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 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 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 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:1.0 SO:unsorted @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 8 -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 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:1.0 SO:unsorted @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 4 -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 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:1.0 SO:unsorted @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 13 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 13 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 4 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 15 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 11 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 9 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 = 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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 4 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 6 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 4 -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:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:120 @SQ SN:1 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 5 -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:1.0 SO:unsorted @SQ SN:0 LN:120 @SQ SN:1 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 7 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --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:1.0 SO:unsorted @SQ SN:0 LN:47 @SQ SN:1 LN:27 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:47 @SQ SN:1 LN:27 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 11 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:61 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 9 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:61 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 8 -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 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:1.0 SO:unsorted @SQ SN:0 LN:23 @SQ SN:1 LN:28 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:23 @SQ SN:1 LN:28 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -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 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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --fr --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" 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 16 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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: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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 2 --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" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -s 1 -u 1 --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 @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --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" 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --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" 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 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 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 2 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 8 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 13 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:3 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 15 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:3 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 16 -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:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 16 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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,.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 3 -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:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -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 3 -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:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 12 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --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 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --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 0 961 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 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:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --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 0 961 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 12 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -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 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --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.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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 6 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 6 -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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 255 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -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 0 316 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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 14 -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 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:1.0 SO:unsorted @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 16 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 8 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 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 79 255 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 6 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index -X 150 --fr --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:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --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 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:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --local --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 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:1.0 SO:unsorted @SQ SN:0 LN:2607 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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:1.0 SO:unsorted @SQ SN:0 LN:2607 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 4 -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 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:1.0 SO:unsorted @SQ SN:0 LN:1906 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -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 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 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:1.0 SO:unsorted @SQ SN:0 LN:1906 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 4 -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 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:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -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 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:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 5 -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 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:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 12 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 10 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 15 -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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --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: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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 3 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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.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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 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 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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 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: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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 14 -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 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:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --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: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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 6 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 14 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 9 -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 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:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 7 -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 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:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 15 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 11 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 10 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 16 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 13 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 5 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 8 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 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:1.0 SO:unsorted @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --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 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 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,.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:1.0 SO:unsorted @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --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,.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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 14 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 4 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 5 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 4 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 14 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:18 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 8 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:18 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 12 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 13 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 14 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 3 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA ./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 11 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 14 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 15 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 10 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 8 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 15 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 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 --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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:25 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:25 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -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:1.0 SO:unsorted @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 13 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:10 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 16 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:10 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 1 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:22 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 15 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:22 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 6 -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 11 -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:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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,.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 6 -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:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -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 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:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --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" 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 7 -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:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 7 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --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 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 8 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:41 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index -I 28 -X 80 --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:1.0 SO:unsorted @SQ SN:0 LN:41 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --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 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 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:1.0 SO:unsorted @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --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 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --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 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --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 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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --nofw --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 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:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --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 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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --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 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --quiet -k 1 --reads-per-batch 3 -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:1.0 SO:unsorted @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -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 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,.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:1.0 SO:unsorted @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --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,.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 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/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" 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 11 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 16 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 1 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 11 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 9 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.0 SO:unsorted @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 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: bowtie2-2.4.1-6.fc39.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.gN8NwE + umask 022 + cd /builddir/build/BUILD + cd bowtie2-2.4.1 + DOCDIR=/builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/doc/bowtie2 + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/doc/bowtie2 + cp -pr AUTHORS /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/doc/bowtie2 + cp -pr MANUAL /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/doc/bowtie2 + cp -pr MANUAL.markdown /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/doc/bowtie2 + cp -pr NEWS /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/doc/bowtie2 + cp -pr TUTORIAL /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/doc/bowtie2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.0dy7nw + umask 022 + cd /builddir/build/BUILD + cd bowtie2-2.4.1 + LICENSEDIR=/builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/licenses/bowtie2 + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/licenses/bowtie2 + cp -pr LICENSE /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64/usr/share/licenses/bowtie2 + RPM_EC=0 ++ jobs -p + exit 0 Provides: bowtie2 = 2.4.1-6.fc39 bowtie2(x86-64) = 2.4.1-6.fc39 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_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgcc_s.so.1(GCC_3.4)(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_1.3.8)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(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_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libtbb.so.2()(64bit) libtbbmalloc_proxy.so.2()(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-2.4.1-6.fc39.x86_64 Provides: bowtie2-debugsource = 2.4.1-6.fc39 bowtie2-debugsource(x86-64) = 2.4.1-6.fc39 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bowtie2-debuginfo-2.4.1-6.fc39.x86_64 Provides: bowtie2-debuginfo = 2.4.1-6.fc39 bowtie2-debuginfo(x86-64) = 2.4.1-6.fc39 debuginfo(build-id) = 346d2a86b600edc04284d5ea6d6842947758c00b debuginfo(build-id) = 5c2b2eb3cef142bc92a5ab25ce64ed7685238d4b debuginfo(build-id) = 71cb4df8271e2733a02ddd04ca96bae9744e85a6 debuginfo(build-id) = 918c2240ed5d2daa7e0395053b9e5c670f6fb1a5 debuginfo(build-id) = e91c312e01c7f7ab830e82ca18f37dba1f9ef4e5 debuginfo(build-id) = f16df23a1a687479e74585cf0d6f7aab166224a7 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bowtie2-debugsource(x86-64) = 2.4.1-6.fc39 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64 Wrote: /builddir/build/RPMS/bowtie2-2.4.1-6.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/bowtie2-debugsource-2.4.1-6.fc39.x86_64.rpm Wrote: /builddir/build/RPMS/bowtie2-debuginfo-2.4.1-6.fc39.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.qiJRzA + umask 022 + cd /builddir/build/BUILD + cd bowtie2-2.4.1 + /usr/bin/rm -rf /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc39.x86_64 + RPM_EC=0 ++ jobs -p + exit 0 Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.9w1gy9 + umask 022 + cd /builddir/build/BUILD + rm -rf bowtie2-2.4.1 bowtie2-2.4.1.gemspec + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bowtie2-2.4.1-6.fc39.src.rpm Finish: build phase for bowtie2-2.4.1-6.fc39.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-x86_64-1676384685.626650/root/var/log/dnf.rpm.log /var/lib/mock/fedora-rawhide-x86_64-1676384685.626650/root/var/log/dnf.librepo.log /var/lib/mock/fedora-rawhide-x86_64-1676384685.626650/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/bowtie2-2.4.1-6.fc39.src.rpm) Config(child) 4 minutes 16 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