Warning: Permanently added '2620:52:6:1161:dead:beef:cafe:c152' (ED25519) to the list of known hosts. You can reproduce this build on your computer by running: sudo dnf install copr-rpmbuild /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/9942910-fedora-rawhide-ppc64le --chroot fedora-rawhide-ppc64le Version: 1.6 PID: 19862 Logging PID: 19864 Task: {'allow_user_ssh': False, 'appstream': False, 'background': True, 'build_id': 9942910, 'buildroot_pkgs': [], 'chroot': 'fedora-rawhide-ppc64le', 'enable_net': False, 'fedora_review': False, 'git_hash': 'a49a1e4a6c99fa003e3764c4546913a33bcb9a19', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/siddhesh/mbp-gcc-16/bowtie2', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'bowtie2', 'package_version': '2.5.1-7', 'project_dirname': 'mbp-gcc-16', 'project_name': 'mbp-gcc-16', 'project_owner': 'siddhesh', 'repo_priority': None, 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/siddhesh/mbp-gcc-16/fedora-rawhide-ppc64le/', 'id': 'copr_base', 'name': 'Copr repository', 'priority': None}, {'baseurl': 'https://kojipkgs.fedoraproject.org/repos/f44-build-side-124978/latest/$basearch/', 'id': 'https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch', 'name': 'Additional repo https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch'}], 'sandbox': 'siddhesh/mbp-gcc-16--siddhesh', 'source_json': {}, 'source_type': None, 'ssh_public_keys': None, 'storage': 0, 'submitter': 'siddhesh', 'tags': [], 'task_id': '9942910-fedora-rawhide-ppc64le', 'timeout': 115200, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/siddhesh/mbp-gcc-16/bowtie2 /var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2 --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/siddhesh/mbp-gcc-16/bowtie2', '/var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2'... Running: git checkout a49a1e4a6c99fa003e3764c4546913a33bcb9a19 -- cmd: ['git', 'checkout', 'a49a1e4a6c99fa003e3764c4546913a33bcb9a19', '--'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2 rc: 0 stdout: stderr: Note: switching to 'a49a1e4a6c99fa003e3764c4546913a33bcb9a19'. 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 a49a1e4 automatic import of bowtie2 Running: dist-git-client sources cmd: ['dist-git-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2 rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading v2.5.1.tar.gz INFO: Reading stdout from command: curl --help all INFO: Calling: curl -H Pragma: -o v2.5.1.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/siddhesh/mbp-gcc-16/bowtie2/v2.5.1.tar.gz/md5/16caf86d239b176a4f367c9f63bd99c0/v2.5.1.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current tail: /var/lib/copr-rpmbuild/main.log: file truncated Dload Upload Total Spent Left Speed 100 10.1M 100 10.1M 0 0 7919k 0 0:00:01 0:00:01 --:--:-- 7925k INFO: Reading stdout from command: md5sum v2.5.1.tar.gz Running (timeout=115200): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2/bowtie2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1766674744.576197 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.6 starting (python version = 3.13.7, NVR = mock-6.6-1.fc42), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2/bowtie2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1766674744.576197 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2/bowtie2.spec) Config(fedora-rawhide-ppc64le) Start: clean chroot Finish: clean chroot Mock Version: 6.6 INFO: Mock Version: 6.6 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1766674744.576197/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-ace70f6b-24d8-4634-a855-5441671381ca INFO: Checking that 2a11093149de2150ffaaa8d82e22bb8bb41aa1aa16b3693f0f97e4921acde31b image matches host's architecture INFO: Copy content of container 2a11093149de2150ffaaa8d82e22bb8bb41aa1aa16b3693f0f97e4921acde31b to /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1766674744.576197/root INFO: mounting 2a11093149de2150ffaaa8d82e22bb8bb41aa1aa16b3693f0f97e4921acde31b with podman image mount INFO: image 2a11093149de2150ffaaa8d82e22bb8bb41aa1aa16b3693f0f97e4921acde31b as /var/lib/containers/storage/overlay/5698018051af4b12832f6465fd120ad4dadc1710c2d5059c663b82048d864076/merged INFO: umounting image 2a11093149de2150ffaaa8d82e22bb8bb41aa1aa16b3693f0f97e4921acde31b (/var/lib/containers/storage/overlay/5698018051af4b12832f6465fd120ad4dadc1710c2d5059c663b82048d864076/merged) with podman image umount INFO: Removing image mock-bootstrap-ace70f6b-24d8-4634-a855-5441671381ca INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1766674744.576197/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.0.1-1.fc44.ppc64le rpm-sequoia-1.10.0-1.fc44.ppc64le dnf5-5.3.0.0-3.fc44.ppc64le dnf5-plugins-5.3.0.0-3.fc44.ppc64le Start: installing minimal buildroot with dnf5 Updating and loading repositories: Additional repo https_kojipkgs_fedorap 100% | 11.3 KiB/s | 3.5 KiB | 00m00s Copr repository 100% | 4.9 KiB/s | 1.5 KiB | 00m00s fedora 100% | 13.2 KiB/s | 4.7 KiB | 00m00s Repositories loaded. 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https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.9 KiB python-srpm-macros noarch 0:3.14-9.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 51.6 KiB qt5-srpm-macros noarch 0:5.15.18-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 500.0 B qt6-srpm-macros noarch 0:6.10.1-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 464.0 B readline ppc64le 0:8.3-2.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 627.5 KiB rpm ppc64le 0:6.0.1-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 4.2 MiB rpm-build-libs ppc64le 0:6.0.1-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 328.0 KiB rpm-libs ppc64le 0:6.0.1-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.2 MiB rpm-plugin-selinux ppc64le 0:6.0.1-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 67.9 KiB rpm-sequoia ppc64le 0:1.10.0-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 4.9 MiB rpm-sign-libs ppc64le 0:6.0.1-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 67.6 KiB rust-srpm-macros noarch 0:28.4-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 5.5 KiB selinux-policy noarch 0:42.19-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 32.0 KiB selinux-policy-targeted noarch 0:42.19-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 18.7 MiB setup noarch 0:2.15.0-27.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 724.9 KiB sqlite-libs ppc64le 0:3.51.0-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.9 MiB systemd-libs ppc64le 0:259-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 3.0 MiB systemd-standalone-sysusers ppc64le 0:259-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 393.6 KiB tpm2-tss ppc64le 0:4.1.3-8.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 2.5 MiB tree-sitter-srpm-macros noarch 0:0.4.2-1.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 8.3 KiB util-linux-core ppc64le 0:2.41.3-8.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 2.5 MiB xxhash-libs ppc64le 0:0.8.3-3.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 85.6 KiB xz-libs ppc64le 1:5.8.1-4.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 265.3 KiB zig-srpm-macros noarch 0:1-5.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.1 KiB zip ppc64le 0:3.0-44.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 889.8 KiB zlib-ng-compat ppc64le 0:2.3.2-2.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 197.3 KiB zstd ppc64le 0:1.5.7-3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 573.9 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 184 packages Total size of inbound packages is 72 MiB. Need to download 0 B. After this operation, 278 MiB extra will be used (install 278 MiB, remove 0 B). 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keyutils-libs-0:1.6.3-6.fc43. 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [181/184] libcom_err-0:1.47.3-3.fc44.pp 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [182/184] libverto-0:0.3.2-11.fc43.ppc6 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [183/184] libssh-config-0:0.11.3-1.fc44 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded [184/184] publicsuffix-list-dafsa-0:202 100% | 0.0 B/s | 0.0 B | 00m00s >>> Already downloaded -------------------------------------------------------------------------------- [184/184] Total 100% | 0.0 B/s | 0.0 B | 00m00s Running transaction Importing OpenPGP key 0x6D9F90A6: UserID : "Fedora (44) " Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary The key was successfully imported. Importing OpenPGP key 0x6D9F90A6: UserID : "Fedora (44) " Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary The key was successfully imported. Importing OpenPGP key 0x31645531: UserID : "Fedora (43) " Fingerprint: C6E7F081CF80E13146676E88829B606631645531 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-43-primary The key was successfully imported. Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. [ 1/186] Verify package files 100% | 160.0 B/s | 184.0 B | 00m01s >>> Running %pretrans scriptlet: filesystem-0:3.18-50.fc43.ppc64le >>> Finished %pretrans scriptlet: filesystem-0:3.18-50.fc43.ppc64le >>> [RPM] /var/lib/mock/fedora-rawhide-ppc64le-1766674744.576197/root/var/cache/dnf/copr_base-28c6ae514b5b287e/packages/bash-5.3.0-2.fc44.ppc64le.rpm: Header OpenPGP V4 RSA/SHA256 signature, key ID 52ac7d71d4a9769d: NOKEY [ 2/186] Prepare transaction 100% | 897.0 B/s | 184.0 B | 00m00s [ 3/186] Installing libgcc-0:16.0.0-0. 100% | 70.3 MiB/s | 288.1 KiB | 00m00s [ 4/186] Installing publicsuffix-list- 100% | 68.2 MiB/s | 69.8 KiB | 00m00s [ 5/186] Installing libssh-config-0:0. 100% | 796.9 KiB/s | 816.0 B | 00m00s [ 6/186] Installing fedora-release-ide 100% | 898.4 KiB/s | 920.0 B | 00m00s [ 7/186] Installing fedora-repos-rawhi 100% | 2.4 MiB/s | 2.4 KiB | 00m00s [ 8/186] Installing fedora-gpg-keys-0: 100% | 11.7 MiB/s | 179.0 KiB | 00m00s [ 9/186] Installing fedora-repos-0:44- 100% | 5.6 MiB/s | 5.7 KiB | 00m00s [ 10/186] Installing fedora-release-com 100% | 8.1 MiB/s | 24.9 KiB | 00m00s [ 11/186] Installing fedora-release-0:4 100% | 15.1 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.0-27.fc44.noarch >>> Finished sysusers scriptlet: setup-0:2.15.0-27.fc44.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 12/186] Installing setup-0:2.15.0-27. 100% | 17.0 MiB/s | 730.6 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 13/186] Installing filesystem-0:3.18- 100% | 709.2 KiB/s | 212.8 KiB | 00m00s [ 14/186] Installing gnulib-l10n-0:2024 100% | 53.9 MiB/s | 661.9 KiB | 00m00s [ 15/186] Installing coreutils-common-0 100% | 115.8 MiB/s | 11.2 MiB | 00m00s [ 16/186] Installing pcre2-syntax-0:10. 100% | 69.4 MiB/s | 284.3 KiB | 00m00s [ 17/186] Installing ncurses-base-0:6.5 100% | 20.3 MiB/s | 353.5 KiB | 00m00s [ 18/186] Installing bash-0:5.3.0-2.fc4 100% | 83.4 MiB/s | 8.9 MiB | 00m00s [ 19/186] Installing glibc-common-0:2.4 100% | 28.0 MiB/s | 1.5 MiB | 00m00s [ 20/186] Installing glibc-gconv-extra- 100% | 122.8 MiB/s | 18.5 MiB | 00m00s [ 21/186] Installing glibc-0:2.42.9000- 100% | 83.2 MiB/s | 11.7 MiB | 00m00s [ 22/186] Installing ncurses-libs-0:6.5 100% | 99.7 MiB/s | 1.5 MiB | 00m00s [ 23/186] Installing glibc-minimal-lang 100% | 121.1 KiB/s | 124.0 B | 00m00s [ 24/186] Installing zlib-ng-compat-0:2 100% | 64.5 MiB/s | 198.1 KiB | 00m00s [ 25/186] Installing bzip2-libs-0:1.0.8 100% | 67.2 MiB/s | 137.7 KiB | 00m00s [ 26/186] Installing libgpg-error-0:1.5 100% | 22.0 MiB/s | 1.0 MiB | 00m00s [ 27/186] Installing libassuan-0:2.5.7- 100% | 70.8 MiB/s | 217.6 KiB | 00m00s [ 28/186] Installing libgcrypt-0:1.11.2 100% | 107.7 MiB/s | 1.5 MiB | 00m00s [ 29/186] Installing readline-0:8.3-2.f 100% | 102.5 MiB/s | 629.7 KiB | 00m00s [ 30/186] Installing xz-libs-1:5.8.1-4. 100% | 65.0 MiB/s | 266.4 KiB | 00m00s [ 31/186] Installing libuuid-0:2.41.3-8 100% | 34.3 MiB/s | 70.3 KiB | 00m00s [ 32/186] Installing gmp-1:6.3.0-4.fc44 100% | 96.2 MiB/s | 788.4 KiB | 00m00s [ 33/186] Installing popt-0:1.19-9.fc43 100% | 26.3 MiB/s | 215.3 KiB | 00m00s [ 34/186] Installing libzstd-0:1.5.7-3. 100% | 109.2 MiB/s | 1.1 MiB | 00m00s [ 35/186] Installing elfutils-libelf-0: 100% | 120.7 MiB/s | 1.2 MiB | 00m00s [ 36/186] Installing npth-0:1.8-3.fc43. 100% | 46.0 MiB/s | 94.2 KiB | 00m00s [ 37/186] Installing libblkid-0:2.41.3- 100% | 86.8 MiB/s | 355.5 KiB | 00m00s [ 38/186] Installing systemd-libs-0:259 100% | 118.5 MiB/s | 3.0 MiB | 00m00s [ 39/186] Installing libxcrypt-0:4.5.2- 100% | 66.4 MiB/s | 339.7 KiB | 00m00s [ 40/186] Installing libsepol-0:3.9-2.f 100% | 115.8 MiB/s | 1.0 MiB | 00m00s [ 41/186] Installing sqlite-libs-0:3.51 100% | 114.1 MiB/s | 1.9 MiB | 00m00s [ 42/186] Installing gnupg2-gpgconf-0:2 100% | 8.1 MiB/s | 323.9 KiB | 00m00s [ 43/186] Installing libattr-0:2.5.2-6. 100% | 33.7 MiB/s | 69.1 KiB | 00m00s [ 44/186] Installing libacl-0:2.3.2-4.f 100% | 33.4 MiB/s | 68.3 KiB | 00m00s [ 45/186] Installing pcre2-0:10.47-1.fc 100% | 103.0 MiB/s | 843.4 KiB | 00m00s [ 46/186] Installing libselinux-0:3.9-5 100% | 65.0 MiB/s | 266.4 KiB | 00m00s [ 47/186] Installing grep-0:3.12-2.fc43 100% | 20.3 MiB/s | 1.0 MiB | 00m00s [ 48/186] Installing sed-0:4.9-6.fc44.p 100% | 19.2 MiB/s | 945.3 KiB | 00m00s [ 49/186] Installing findutils-1:4.10.0 100% | 35.9 MiB/s | 2.0 MiB | 00m00s [ 50/186] Installing libtasn1-0:4.20.0- 100% | 54.2 MiB/s | 221.9 KiB | 00m00s [ 51/186] Installing libunistring-0:1.1 100% | 117.0 MiB/s | 1.9 MiB | 00m00s [ 52/186] Installing libidn2-0:2.3.8-2. 100% | 30.7 MiB/s | 566.4 KiB | 00m00s [ 53/186] Installing crypto-policies-0: 100% | 8.6 MiB/s | 157.7 KiB | 00m00s [ 54/186] Installing xz-1:5.8.1-4.fc44. 100% | 24.8 MiB/s | 1.4 MiB | 00m00s [ 55/186] Installing libmount-0:2.41.3- 100% | 89.4 MiB/s | 549.2 KiB | 00m00s [ 56/186] Installing gnupg2-verify-0:2. 100% | 10.0 MiB/s | 429.7 KiB | 00m00s [ 57/186] Installing dwz-0:0.16-2.fc43. 100% | 10.0 MiB/s | 388.0 KiB | 00m00s [ 58/186] Installing mpfr-0:4.2.2-2.fc4 100% | 81.3 MiB/s | 915.3 KiB | 00m00s [ 59/186] Installing gawk-0:5.3.2-2.fc4 100% | 44.9 MiB/s | 2.8 MiB | 00m00s [ 60/186] Installing libksba-0:1.6.7-4. 100% | 86.1 MiB/s | 529.0 KiB | 00m00s [ 61/186] Installing unzip-0:6.0-68.fc4 100% | 13.1 MiB/s | 537.4 KiB | 00m00s [ 62/186] Installing file-libs-0:5.46-8 100% | 182.8 MiB/s | 11.9 MiB | 00m00s [ 63/186] Installing file-0:5.46-8.fc44 100% | 3.6 MiB/s | 141.6 KiB | 00m00s [ 64/186] Installing diffutils-0:3.12-3 100% | 31.8 MiB/s | 1.7 MiB | 00m00s [ 65/186] Installing libcap-ng-0:0.8.5- 100% | 52.8 MiB/s | 162.1 KiB | 00m00s [ 66/186] Installing audit-libs-0:4.1.2 100% | 90.0 MiB/s | 553.2 KiB | 00m00s [ 67/186] Installing libsemanage-0:3.9- 100% | 83.1 MiB/s | 425.7 KiB | 00m00s [ 68/186] Installing libsmartcols-0:2.4 100% | 70.9 MiB/s | 290.5 KiB | 00m00s [ 69/186] Installing libeconf-0:0.7.9-2 100% | 40.3 MiB/s | 82.5 KiB | 00m00s [ 70/186] Installing pam-libs-0:1.7.1-3 100% | 70.5 MiB/s | 288.6 KiB | 00m00s [ 71/186] Installing libcap-0:2.77-1.fc 100% | 11.9 MiB/s | 512.9 KiB | 00m00s [ 72/186] Installing alternatives-0:1.3 100% | 2.5 MiB/s | 91.7 KiB | 00m00s [ 73/186] Installing lua-libs-0:5.4.8-4 100% | 77.2 MiB/s | 395.3 KiB | 00m00s [ 74/186] Installing json-c-0:0.18-7.fc 100% | 68.3 MiB/s | 139.8 KiB | 00m00s [ 75/186] Installing libffi-0:3.5.2-1.f 100% | 85.2 MiB/s | 349.0 KiB | 00m00s [ 76/186] Installing p11-kit-0:0.25.8-1 100% | 44.0 MiB/s | 2.9 MiB | 00m00s [ 77/186] Installing p11-kit-trust-0:0. 100% | 12.1 MiB/s | 595.9 KiB | 00m00s [ 78/186] Installing ngtcp2-0:1.18.0-1. 100% | 79.4 MiB/s | 406.7 KiB | 00m00s [ 79/186] Installing openssl-libs-1:3.5 100% | 127.5 MiB/s | 9.0 MiB | 00m00s [ 80/186] Installing coreutils-0:9.9-1. 100% | 81.3 MiB/s | 9.4 MiB | 00m00s [ 81/186] Installing ca-certificates-0: 100% | 728.8 KiB/s | 2.5 MiB | 00m03s [ 82/186] Installing gzip-0:1.14-1.fc44 100% | 7.9 MiB/s | 443.1 KiB | 00m00s [ 83/186] Installing rpm-sequoia-0:1.10 100% | 127.7 MiB/s | 4.9 MiB | 00m00s [ 84/186] Installing libfsverity-0:1.6- 100% | 33.7 MiB/s | 69.1 KiB | 00m00s [ 85/186] Installing libevent-0:2.1.12- 100% | 110.0 MiB/s | 1.2 MiB | 00m00s [ 86/186] Installing ngtcp2-crypto-ossl 100% | 33.3 MiB/s | 68.1 KiB | 00m00s [ 87/186] Installing util-linux-core-0: 100% | 40.0 MiB/s | 2.5 MiB | 00m00s [ 88/186] Installing zip-0:3.0-44.fc43. 100% | 19.8 MiB/s | 893.7 KiB | 00m00s [ 89/186] Installing gnupg2-keyboxd-0:2 100% | 32.4 MiB/s | 298.5 KiB | 00m00s [ 90/186] Installing libpsl-0:0.21.5-6. 100% | 43.4 MiB/s | 133.2 KiB | 00m00s [ 91/186] Installing tar-2:1.35-6.fc43. 100% | 48.9 MiB/s | 3.1 MiB | 00m00s [ 92/186] Installing linkdupes-0:0.7.2- 100% | 20.2 MiB/s | 908.5 KiB | 00m00s [ 93/186] Installing libselinux-utils-0 100% | 28.3 MiB/s | 1.4 MiB | 00m00s [ 94/186] Installing liblastlog2-0:2.41 100% | 17.0 MiB/s | 139.4 KiB | 00m00s [ 95/186] Installing systemd-standalone 100% | 10.1 MiB/s | 394.1 KiB | 00m00s [ 96/186] Installing libusb1-0:1.0.29-4 100% | 19.9 MiB/s | 244.4 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.ppc64le >>> Finished sysusers scriptlet: tpm2-tss-0:4.1.3-8.fc43.ppc64le >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [ 97/186] Installing tpm2-tss-0:4.1.3-8 100% | 112.2 MiB/s | 2.5 MiB | 00m00s [ 98/186] Installing ima-evm-utils-libs 100% | 45.8 MiB/s | 93.9 KiB | 00m00s [ 99/186] Installing gnupg2-gpg-agent-0 100% | 19.1 MiB/s | 979.0 KiB | 00m00s [100/186] Installing libfdisk-0:2.41.3- 100% | 94.5 MiB/s | 483.9 KiB | 00m00s [101/186] Installing nettle-0:3.10.1-2. 100% | 104.3 MiB/s | 960.9 KiB | 00m00s [102/186] Installing gnutls-0:3.8.11-6. 100% | 119.8 MiB/s | 4.1 MiB | 00m00s [103/186] Installing libxml2-0:2.12.10- 100% | 41.2 MiB/s | 2.3 MiB | 00m00s [104/186] Installing bzip2-0:1.0.8-21.f 100% | 4.5 MiB/s | 175.7 KiB | 00m00s [105/186] Installing add-determinism-0: 100% | 43.2 MiB/s | 2.4 MiB | 00m00s [106/186] Installing cpio-0:2.15-6.fc43 100% | 22.7 MiB/s | 1.2 MiB | 00m00s [107/186] Installing librtas-0:2.0.6-5. 100% | 20.0 MiB/s | 307.6 KiB | 00m00s [108/186] Installing util-linux-0:2.41. 100% | 57.6 MiB/s | 7.0 MiB | 00m00s [109/186] Installing policycoreutils-0: 100% | 18.5 MiB/s | 1.3 MiB | 00m00s [110/186] Installing selinux-policy-0:4 100% | 1.2 MiB/s | 33.6 KiB | 00m00s [111/186] Installing selinux-policy-tar 100% | 51.4 MiB/s | 14.9 MiB | 00m00s [112/186] Installing build-reproducibil 100% | 1.5 MiB/s | 1.5 KiB | 00m00s [113/186] Installing libpkgconf-0:2.3.0 100% | 65.9 MiB/s | 135.0 KiB | 00m00s [114/186] Installing pkgconf-0:2.3.0-3. 100% | 2.7 MiB/s | 114.8 KiB | 00m00s [115/186] Installing ed-0:1.22.3-1.fc44 100% | 4.1 MiB/s | 159.1 KiB | 00m00s [116/186] Installing patch-0:2.8-3.fc44 100% | 6.8 MiB/s | 263.9 KiB | 00m00s [117/186] Installing libatomic-0:16.0.0 100% | 33.7 MiB/s | 69.0 KiB | 00m00s [118/186] Installing libstdc++-0:16.0.0 100% | 126.3 MiB/s | 3.9 MiB | 00m00s [119/186] Installing rpm-libs-0:6.0.1-1 100% | 102.0 MiB/s | 1.2 MiB | 00m00s [120/186] Installing zstd-0:1.5.7-3.fc4 100% | 13.4 MiB/s | 577.4 KiB | 00m00s [121/186] Installing lz4-libs-0:1.10.0- 100% | 64.0 MiB/s | 262.2 KiB | 00m00s [122/186] Installing libarchive-0:3.8.4 100% | 105.6 MiB/s | 1.3 MiB | 00m00s [123/186] Installing jansson-0:2.14-3.f 100% | 51.6 MiB/s | 158.4 KiB | 00m00s [124/186] Installing libgomp-0:16.0.0-0 100% | 106.8 MiB/s | 655.9 KiB | 00m00s [125/186] Installing libtool-ltdl-0:2.5 100% | 46.3 MiB/s | 94.9 KiB | 00m00s [126/186] Installing gdbm-libs-1:1.23-1 100% | 76.6 MiB/s | 235.2 KiB | 00m00s [127/186] Installing cyrus-sasl-lib-0:2 100% | 48.6 MiB/s | 2.9 MiB | 00m00s [128/186] Installing openldap-0:2.6.10- 100% | 87.3 MiB/s | 893.7 KiB | 00m00s [129/186] Installing gnupg2-dirmngr-0:2 100% | 17.1 MiB/s | 840.8 KiB | 00m00s [130/186] Installing gnupg2-0:2.4.8-4.f 100% | 73.4 MiB/s | 6.9 MiB | 00m00s [131/186] Installing rpm-sign-libs-0:6. 100% | 33.4 MiB/s | 68.5 KiB | 00m00s [132/186] Installing gpgverify-0:2.2-3. 100% | 9.2 MiB/s | 9.4 KiB | 00m00s [133/186] Installing xxhash-libs-0:0.8. 100% | 42.5 MiB/s | 87.0 KiB | 00m00s [134/186] Installing libbrotli-0:1.2.0- 100% | 92.2 MiB/s | 1.0 MiB | 00m00s [135/186] Installing libnghttp2-0:1.68. 100% | 48.6 MiB/s | 199.0 KiB | 00m00s [136/186] Installing libnghttp3-0:1.14. 100% | 40.6 MiB/s | 207.9 KiB | 00m00s [137/186] Installing keyutils-libs-0:1. 100% | 32.4 MiB/s | 99.4 KiB | 00m00s [138/186] Installing libcom_err-0:1.47. 100% | 36.5 MiB/s | 112.1 KiB | 00m00s [139/186] Installing libverto-0:0.3.2-1 100% | 17.3 MiB/s | 70.9 KiB | 00m00s [140/186] Installing krb5-libs-0:1.21.3 100% | 78.1 MiB/s | 3.0 MiB | 00m00s [141/186] Installing libssh-0:0.11.3-1. 100% | 77.8 MiB/s | 717.3 KiB | 00m00s [142/186] Installing libcurl-0:8.18.0~r 100% | 100.7 MiB/s | 1.2 MiB | 00m00s [143/186] Installing curl-0:8.18.0~rc2- 100% | 9.8 MiB/s | 530.2 KiB | 00m00s [144/186] Installing rpm-0:6.0.1-1.fc44 100% | 30.4 MiB/s | 2.8 MiB | 00m00s [145/186] Installing cmake-srpm-macros- 100% | 785.2 KiB/s | 804.0 B | 00m00s [146/186] Installing efi-srpm-macros-0: 100% | 20.1 MiB/s | 41.2 KiB | 00m00s [147/186] Installing java-srpm-macros-0 100% | 1.1 MiB/s | 1.1 KiB | 00m00s [148/186] Installing lua-srpm-macros-0: 100% | 1.9 MiB/s | 1.9 KiB | 00m00s [149/186] Installing tree-sitter-srpm-m 100% | 4.5 MiB/s | 9.3 KiB | 00m00s [150/186] Installing zig-srpm-macros-0: 100% | 1.6 MiB/s | 1.7 KiB | 00m00s [151/186] Installing filesystem-srpm-ma 100% | 19.0 MiB/s | 38.9 KiB | 00m00s [152/186] Installing elfutils-default-y 100% | 408.6 KiB/s | 2.0 KiB | 00m00s [153/186] Installing elfutils-libs-0:0. 100% | 95.1 MiB/s | 876.4 KiB | 00m00s [154/186] Installing elfutils-debuginfo 100% | 3.6 MiB/s | 145.7 KiB | 00m00s [155/186] Installing binutils-0:2.45.50 100% | 117.7 MiB/s | 32.8 MiB | 00m00s [156/186] Installing elfutils-0:0.194-2 100% | 55.7 MiB/s | 3.5 MiB | 00m00s [157/186] Installing gdb-minimal-0:16.3 100% | 104.5 MiB/s | 15.7 MiB | 00m00s [158/186] Installing debugedit-0:5.2-3. 100% | 8.9 MiB/s | 384.9 KiB | 00m00s [159/186] Installing rpm-build-libs-0:6 100% | 80.3 MiB/s | 328.8 KiB | 00m00s [160/186] Installing pkgconf-m4-0:2.3.0 100% | 14.5 MiB/s | 14.8 KiB | 00m00s [161/186] Installing pkgconf-pkg-config 100% | 49.3 KiB/s | 1.8 KiB | 00m00s [162/186] Installing rust-srpm-macros-0 100% | 6.2 MiB/s | 6.4 KiB | 00m00s [163/186] Installing qt6-srpm-macros-0: 100% | 722.7 KiB/s | 740.0 B | 00m00s [164/186] Installing qt5-srpm-macros-0: 100% | 757.8 KiB/s | 776.0 B | 00m00s [165/186] Installing perl-srpm-macros-0 100% | 1.1 MiB/s | 1.1 KiB | 00m00s [166/186] Installing package-notes-srpm 100% | 2.0 MiB/s | 2.0 KiB | 00m00s [167/186] Installing openblas-srpm-macr 100% | 382.8 KiB/s | 392.0 B | 00m00s [168/186] Installing ocaml-srpm-macros- 100% | 2.1 MiB/s | 2.1 KiB | 00m00s [169/186] Installing kernel-srpm-macros 100% | 2.3 MiB/s | 2.3 KiB | 00m00s [170/186] Installing gnat-srpm-macros-0 100% | 1.2 MiB/s | 1.3 KiB | 00m00s [171/186] Installing ghc-srpm-macros-0: 100% | 1.0 MiB/s | 1.0 KiB | 00m00s [172/186] Installing gap-srpm-macros-0: 100% | 2.6 MiB/s | 2.7 KiB | 00m00s [173/186] Installing fpc-srpm-macros-0: 100% | 410.2 KiB/s | 420.0 B | 00m00s [174/186] Installing ansible-srpm-macro 100% | 17.7 MiB/s | 36.2 KiB | 00m00s [175/186] Installing rpm-build-0:6.0.1- 100% | 14.6 MiB/s | 672.5 KiB | 00m00s [176/186] Installing pyproject-srpm-mac 100% | 1.2 MiB/s | 2.5 KiB | 00m00s [177/186] Installing redhat-rpm-config- 100% | 30.9 MiB/s | 189.9 KiB | 00m00s [178/186] Installing forge-srpm-macros- 100% | 19.7 MiB/s | 40.3 KiB | 00m00s [179/186] Installing fonts-srpm-macros- 100% | 27.8 MiB/s | 57.0 KiB | 00m00s [180/186] Installing go-srpm-macros-0:3 100% | 30.8 MiB/s | 63.0 KiB | 00m00s [181/186] Installing R-srpm-macros-0:1. 100% | 3.9 MiB/s | 4.0 KiB | 00m00s [182/186] Installing python-srpm-macros 100% | 25.9 MiB/s | 52.9 KiB | 00m00s [183/186] Installing rpm-plugin-selinux 100% | 33.6 MiB/s | 68.9 KiB | 00m00s [184/186] Installing which-0:2.23-3.fc4 100% | 3.1 MiB/s | 125.5 KiB | 00m00s [185/186] Installing shadow-utils-2:4.1 100% | 46.3 MiB/s | 4.9 MiB | 00m00s [186/186] Installing info-0:7.2-7.fc44. 100% | 34.2 KiB/s | 485.8 KiB | 00m14s Warning: skipped OpenPGP checks for 179 packages from repositories: copr_base, https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: R-srpm-macros-1.3.0-1.fc44.noarch add-determinism-0.7.2-2.fc44.ppc64le alternatives-1.33-3.fc44.ppc64le ansible-srpm-macros-1-18.1.fc43.noarch audit-libs-4.1.2-2.fc44.ppc64le bash-5.3.0-2.fc44.ppc64le binutils-2.45.50-12.fc44.ppc64le build-reproducibility-srpm-macros-0.7.2-2.fc44.noarch bzip2-1.0.8-21.fc43.ppc64le bzip2-libs-1.0.8-21.fc43.ppc64le ca-certificates-2025.2.80_v9.0.304-2.fc44.noarch cmake-srpm-macros-3.31.10-3.fc44.noarch coreutils-9.9-1.fc44.ppc64le coreutils-common-9.9-1.fc44.ppc64le cpio-2.15-6.fc43.ppc64le crypto-policies-20251128-1.git19878fe.fc44.noarch curl-8.18.0~rc2-1.fc44.ppc64le cyrus-sasl-lib-2.1.28-33.fc44.ppc64le debugedit-5.2-3.fc44.ppc64le diffutils-3.12-3.fc43.ppc64le dwz-0.16-2.fc43.ppc64le ed-1.22.3-1.fc44.ppc64le efi-srpm-macros-6-5.fc44.noarch elfutils-0.194-2.fc44.ppc64le elfutils-debuginfod-client-0.194-2.fc44.ppc64le elfutils-default-yama-scope-0.194-2.fc44.noarch elfutils-libelf-0.194-2.fc44.ppc64le elfutils-libs-0.194-2.fc44.ppc64le fedora-gpg-keys-44-0.1.noarch fedora-release-44-0.10.noarch fedora-release-common-44-0.10.noarch fedora-release-identity-basic-44-0.10.noarch fedora-repos-44-0.1.noarch fedora-repos-rawhide-44-0.1.noarch file-5.46-8.fc44.ppc64le file-libs-5.46-8.fc44.ppc64le filesystem-3.18-50.fc43.ppc64le filesystem-srpm-macros-3.18-50.fc43.noarch findutils-4.10.0-6.fc43.ppc64le fonts-srpm-macros-5.0.0-1.fc44.noarch forge-srpm-macros-0.4.0-3.fc43.noarch fpc-srpm-macros-1.3-15.fc43.noarch gap-srpm-macros-2-1.fc44.noarch gawk-5.3.2-2.fc43.ppc64le gdb-minimal-16.3-6.fc44.ppc64le gdbm-libs-1.23-10.fc43.ppc64le ghc-srpm-macros-1.9.2-3.fc43.noarch glibc-2.42.9000-17.fc44.ppc64le glibc-common-2.42.9000-17.fc44.ppc64le glibc-gconv-extra-2.42.9000-17.fc44.ppc64le glibc-minimal-langpack-2.42.9000-17.fc44.ppc64le gmp-6.3.0-4.fc44.ppc64le gnat-srpm-macros-6-8.fc43.noarch gnulib-l10n-20241231-1.fc44.noarch gnupg2-2.4.8-4.fc43.ppc64le gnupg2-dirmngr-2.4.8-4.fc43.ppc64le gnupg2-gpg-agent-2.4.8-4.fc43.ppc64le gnupg2-gpgconf-2.4.8-4.fc43.ppc64le gnupg2-keyboxd-2.4.8-4.fc43.ppc64le gnupg2-verify-2.4.8-4.fc43.ppc64le gnutls-3.8.11-6.fc44.ppc64le go-srpm-macros-3.8.0-1.fc44.noarch gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98 gpg-pubkey-c6e7f081cf80e13146676e88829b606631645531-66b6dccf gpgverify-2.2-3.fc43.noarch grep-3.12-2.fc43.ppc64le gzip-1.14-1.fc44.ppc64le ima-evm-utils-libs-1.6.2-7.fc44.ppc64le info-7.2-7.fc44.ppc64le jansson-2.14-3.fc43.ppc64le java-srpm-macros-1-7.fc43.noarch json-c-0.18-7.fc43.ppc64le kernel-srpm-macros-1.0-27.fc43.noarch keyutils-libs-1.6.3-6.fc43.ppc64le krb5-libs-1.21.3-10.fc44.ppc64le libacl-2.3.2-4.fc44.ppc64le libarchive-3.8.4-1.fc44.ppc64le libassuan-2.5.7-4.fc43.ppc64le libatomic-16.0.0-0.3.fc44.ppc64le libattr-2.5.2-6.fc43.ppc64le libblkid-2.41.3-8.fc44.ppc64le libbrotli-1.2.0-1.fc44.ppc64le libcap-2.77-1.fc44.ppc64le libcap-ng-0.8.5-8.fc44.ppc64le libcom_err-1.47.3-3.fc44.ppc64le libcurl-8.18.0~rc2-1.fc44.ppc64le libeconf-0.7.9-2.fc43.ppc64le libevent-2.1.12-16.fc43.ppc64le libfdisk-2.41.3-8.fc44.ppc64le libffi-3.5.2-1.fc44.ppc64le libfsverity-1.6-3.fc43.ppc64le libgcc-16.0.0-0.3.fc44.ppc64le libgcrypt-1.11.2-1.fc44.ppc64le libgomp-16.0.0-0.3.fc44.ppc64le libgpg-error-1.58-1.fc44.ppc64le libidn2-2.3.8-2.fc43.ppc64le libksba-1.6.7-4.fc43.ppc64le liblastlog2-2.41.3-8.fc44.ppc64le libmount-2.41.3-8.fc44.ppc64le libnghttp2-1.68.0-2.fc44.ppc64le libnghttp3-1.14.0-1.fc44.ppc64le libpkgconf-2.3.0-3.fc43.ppc64le libpsl-0.21.5-6.fc43.ppc64le librtas-2.0.6-5.fc44.ppc64le libselinux-3.9-5.fc44.ppc64le libselinux-utils-3.9-5.fc44.ppc64le libsemanage-3.9-4.fc44.ppc64le libsepol-3.9-2.fc43.ppc64le libsmartcols-2.41.3-8.fc44.ppc64le libssh-0.11.3-1.fc44.ppc64le libssh-config-0.11.3-1.fc44.noarch libstdc++-16.0.0-0.3.fc44.ppc64le libtasn1-4.20.0-2.fc43.ppc64le libtool-ltdl-2.5.4-9.fc44.ppc64le libunistring-1.1-10.fc43.ppc64le libusb1-1.0.29-4.fc44.ppc64le libuuid-2.41.3-8.fc44.ppc64le libverto-0.3.2-11.fc43.ppc64le libxcrypt-4.5.2-2.fc44.ppc64le libxml2-2.12.10-5.fc44.ppc64le libzstd-1.5.7-3.fc44.ppc64le linkdupes-0.7.2-2.fc44.ppc64le lua-libs-5.4.8-4.fc44.ppc64le lua-srpm-macros-1-16.fc43.noarch lz4-libs-1.10.0-3.fc43.ppc64le mpfr-4.2.2-2.fc43.ppc64le ncurses-base-6.5-8.20250614.fc44.noarch ncurses-libs-6.5-8.20250614.fc44.ppc64le nettle-3.10.1-2.fc43.ppc64le ngtcp2-1.18.0-1.fc44.ppc64le ngtcp2-crypto-ossl-1.18.0-1.fc44.ppc64le npth-1.8-3.fc43.ppc64le ocaml-srpm-macros-11-2.fc43.noarch openblas-srpm-macros-2-20.fc43.noarch openldap-2.6.10-4.fc44.ppc64le openssl-libs-3.5.4-1.fc44.ppc64le p11-kit-0.25.8-1.fc44.ppc64le p11-kit-trust-0.25.8-1.fc44.ppc64le package-notes-srpm-macros-0.5-14.fc43.noarch pam-libs-1.7.1-3.fc43.ppc64le patch-2.8-3.fc44.ppc64le pcre2-10.47-1.fc44.ppc64le pcre2-syntax-10.47-1.fc44.noarch perl-srpm-macros-1-60.fc43.noarch pkgconf-2.3.0-3.fc43.ppc64le pkgconf-m4-2.3.0-3.fc43.noarch pkgconf-pkg-config-2.3.0-3.fc43.ppc64le policycoreutils-3.9-5.fc44.ppc64le popt-1.19-9.fc43.ppc64le publicsuffix-list-dafsa-20250616-2.fc43.noarch pyproject-srpm-macros-1.18.6-1.fc44.noarch python-srpm-macros-3.14-9.fc44.noarch qt5-srpm-macros-5.15.18-1.fc44.noarch qt6-srpm-macros-6.10.1-1.fc44.noarch readline-8.3-2.fc43.ppc64le redhat-rpm-config-343-19.fc44.noarch rpm-6.0.1-1.fc44.ppc64le rpm-build-6.0.1-1.fc44.ppc64le rpm-build-libs-6.0.1-1.fc44.ppc64le rpm-libs-6.0.1-1.fc44.ppc64le rpm-plugin-selinux-6.0.1-1.fc44.ppc64le rpm-sequoia-1.10.0-1.fc44.ppc64le rpm-sign-libs-6.0.1-1.fc44.ppc64le rust-srpm-macros-28.4-1.fc44.noarch sed-4.9-6.fc44.ppc64le selinux-policy-42.19-1.fc44.noarch selinux-policy-targeted-42.19-1.fc44.noarch setup-2.15.0-27.fc44.noarch shadow-utils-4.18.0-7.fc44.ppc64le sqlite-libs-3.51.0-1.fc44.ppc64le systemd-libs-259-1.fc44.ppc64le systemd-standalone-sysusers-259-1.fc44.ppc64le tar-1.35-6.fc43.ppc64le tpm2-tss-4.1.3-8.fc43.ppc64le tree-sitter-srpm-macros-0.4.2-1.fc43.noarch unzip-6.0-68.fc44.ppc64le util-linux-2.41.3-8.fc44.ppc64le util-linux-core-2.41.3-8.fc44.ppc64le which-2.23-3.fc43.ppc64le xxhash-libs-0.8.3-3.fc43.ppc64le xz-5.8.1-4.fc44.ppc64le xz-libs-5.8.1-4.fc44.ppc64le zig-srpm-macros-1-5.fc43.noarch zip-3.0-44.fc43.ppc64le zlib-ng-compat-2.3.2-2.fc44.ppc64le zstd-1.5.7-3.fc44.ppc64le Start: buildsrpm Start: rpmbuild -bs Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1753228800 Wrote: /builddir/build/SRPMS/bowtie2-2.5.1-7.fc44.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-ppc64le-1766674744.576197/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-83z31w9k/bowtie2/bowtie2.spec) Config(child) 0 minutes 42 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/bowtie2-2.5.1-7.fc44.src.rpm) Config(fedora-rawhide-ppc64le) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1766674744.576197/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1766674744.576197/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1766674744.576197/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.0.1-1.fc44.ppc64le rpm-sequoia-1.10.0-1.fc44.ppc64le dnf5-5.3.0.0-3.fc44.ppc64le dnf5-plugins-5.3.0.0-3.fc44.ppc64le Finish: chroot init Start: build phase for bowtie2-2.5.1-7.fc44.src.rpm Start: build setup for bowtie2-2.5.1-7.fc44.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1753228800 Wrote: /builddir/build/SRPMS/bowtie2-2.5.1-7.fc44.src.rpm Updating and loading repositories: Additional repo https_kojipkgs_fedorap 100% | 7.7 KiB/s | 3.5 KiB | 00m00s Copr repository 100% | 3.4 KiB/s | 1.5 KiB | 00m00s fedora 100% | 9.4 KiB/s | 4.7 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: gcc-c++ ppc64le 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 47.7 MiB help2man noarch 0:1.49.3-8.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 415.6 KiB libasan ppc64le 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 2.2 MiB libubsan ppc64le 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 669.0 KiB make ppc64le 1:4.4.1-11.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.9 MiB perl-Clone ppc64le 0:0.47-4.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 80.1 KiB perl-File-Which noarch 0:1.27-14.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 30.4 KiB perl-FindBin noarch 0:1.54-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 6.8 KiB perl-Sys-Hostname ppc64le 0:1.25-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 71.5 KiB perl-Test-Deep noarch 0:1.205-2.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 265.7 KiB perl-generators noarch 0:1.16-8.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 21.8 KiB perl-interpreter ppc64le 4:5.42.0-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 174.5 KiB perl-lib ppc64le 0:0.65-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 8.5 KiB python3 ppc64le 0:3.14.2-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 84.8 KiB simde-devel noarch 0:0.8.2-5.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 7.9 MiB zlib-ng-compat-devel ppc64le 0:2.3.2-2.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 107.0 KiB Installing dependencies: annobin-docs noarch 0:13.04-3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 99.2 KiB annobin-plugin-gcc ppc64le 0:13.04-3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 707.4 KiB cmake-filesystem ppc64le 0:3.31.10-3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 0.0 B cpp ppc64le 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 41.7 MiB expat ppc64le 0:2.7.3-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 424.7 KiB gcc ppc64le 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 117.9 MiB gcc-plugin-annobin ppc64le 0:16.0.0-0.3.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 68.9 KiB glibc-devel ppc64le 0:2.42.9000-17.fc44 fedora 3.7 MiB groff-base ppc64le 0:1.23.0-11.fc44 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https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 27.7 KiB perl-JSON-PP noarch 1:4.16-522.fc44 fedora 141.9 KiB perl-MIME-Base32 noarch 0:1.303-24.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 30.7 KiB perl-MIME-Base64 ppc64le 0:3.16-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 93.7 KiB perl-Math-BigInt noarch 1:2.0050.03-3.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.1 MiB perl-Math-Complex noarch 0:1.63-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 85.1 KiB perl-Net-SSLeay ppc64le 0:1.94-11.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.5 MiB perl-POSIX ppc64le 0:2.23-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 328.3 KiB perl-PathTools ppc64le 0:3.94-520.fc43 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1:3.37-521.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 243.1 KiB perl-Symbol noarch 0:1.09-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 6.8 KiB perl-Term-ANSIColor noarch 0:5.01-521.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 97.5 KiB perl-Term-Cap noarch 0:1.18-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 29.3 KiB perl-Term-Table noarch 0:0.025-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 78.0 KiB perl-Test-Simple noarch 3:1.302219-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.8 MiB perl-Text-ParseWords noarch 0:3.31-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 13.6 KiB perl-Text-Tabs+Wrap noarch 0:2024.001-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 22.6 KiB perl-Time-HiRes ppc64le 4:1.9778-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 151.5 KiB perl-Time-Local noarch 2:1.350-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 69.0 KiB perl-URI noarch 0:5.34-2.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 268.0 KiB perl-base noarch 0:2.27-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 12.6 KiB perl-constant noarch 0:1.33-521.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 26.2 KiB perl-if noarch 0:0.61.000-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 5.8 KiB perl-libnet noarch 0:3.15-521.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 289.4 KiB perl-libs ppc64le 4:5.42.0-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 12.3 MiB perl-locale noarch 0:1.13-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 6.1 KiB perl-macros noarch 4:5.42.0-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 5.5 KiB perl-mro ppc64le 0:1.29-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 81.2 KiB perl-overload noarch 0:1.40-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 71.6 KiB perl-overloading noarch 0:0.02-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 4.9 KiB perl-parent noarch 1:0.244-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 10.3 KiB perl-podlators noarch 1:6.0.2-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 317.5 KiB perl-threads ppc64le 1:2.43-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 134.9 KiB perl-vars noarch 0:1.05-520.fc43 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 3.9 KiB python-pip-wheel noarch 0:25.3-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.2 MiB python3-libs ppc64le 0:3.14.2-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 46.4 MiB tzdata noarch 0:2025c-1.fc44 https_kojipkgs_fedoraproject_org_repos_f44_build_side_124978_latest_basearch 1.2 MiB Transaction Summary: Installing: 100 packages Total size of inbound packages is 99 MiB. Need to download 825 KiB. After this operation, 355 MiB extra will be used (install 355 MiB, remove 0 B). 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Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1753228800 Wrote: /builddir/build/SRPMS/bowtie2-2.5.1-7.fc44.src.rpm Updating and loading repositories: Additional repo https_kojipkgs_fedorap 100% | 2.9 KiB/s | 3.5 KiB | 00m01s Copr repository 100% | 1.3 KiB/s | 1.5 KiB | 00m01s fedora 100% | 3.7 KiB/s | 4.7 KiB | 00m01s Repositories loaded. Package "gcc-c++-16.0.0-0.3.fc44.ppc64le" is already installed. Package "help2man-1.49.3-8.fc43.noarch" is already installed. Package "libasan-16.0.0-0.3.fc44.ppc64le" is already installed. Package "libubsan-16.0.0-0.3.fc44.ppc64le" is already installed. Package "make-1:4.4.1-11.fc43.ppc64le" is already installed. Package "perl-Clone-0.47-4.fc43.ppc64le" is already installed. Package "perl-File-Which-1.27-14.fc43.noarch" is already installed. Package "perl-FindBin-1.54-520.fc43.noarch" is already installed. Package "perl-Sys-Hostname-1.25-520.fc43.ppc64le" is already installed. Package "perl-Test-Deep-1.205-2.fc43.noarch" is already installed. Package "perl-lib-0.65-520.fc43.ppc64le" is already installed. Package "perl-generators-1.16-8.fc43.noarch" is already installed. Package "perl-interpreter-4:5.42.0-520.fc43.ppc64le" is already installed. Package "python3-3.14.2-1.fc44.ppc64le" is already installed. Package "simde-devel-0.8.2-5.fc43.noarch" is already installed. Package "zlib-ng-compat-devel-2.3.2-2.fc44.ppc64le" is already installed. Nothing to do. Finish: build setup for bowtie2-2.5.1-7.fc44.src.rpm Start: rpmbuild bowtie2-2.5.1-7.fc44.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1753228800 Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.da8uMq Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.tmjOBn + umask 022 + cd /builddir/build/BUILD/bowtie2-2.5.1-build + cd /builddir/build/BUILD/bowtie2-2.5.1-build + rm -rf bowtie2-2.5.1 + /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/v2.5.1.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd bowtie2-2.5.1 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + rm -rf third_party + sed -e 's/“/"/g' -e 's/”/"/g' -i processor_support.h + sed -i '1s|/usr/bin/env perl|/usr/bin/perl|' bowtie2 + for file in bowtie2-{build,inspect} + sed -i '1s|/usr/bin/env python3|/usr/bin/python3|' bowtie2-build + for file in bowtie2-{build,inspect} + sed -i '1s|/usr/bin/env python3|/usr/bin/python3|' bowtie2-inspect + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.HFbOQZ + umask 022 + cd /builddir/build/BUILD/bowtie2-2.5.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bowtie2-2.5.1 + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -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 + export POPCNT_CAPABILITY=0 + POPCNT_CAPABILITY=0 + export NO_TBB=1 + NO_TBB=1 + /usr/bin/make -O -j5 V=1 VERBOSE=1 all g++ -O3 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \ -Ithird_party \ -o bowtie2-inspect-s bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lpthread -lz g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-build-l bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lpthread -lz In file included from blockwise_sa.h:41, from bt2_idx.h:42, from bt2_build.cpp:28: diff_sample.h: In instantiation of ‘EList getDeltaMap(T, const EList&) [with T = unsigned int]’: required from ‘DifferenceCoverSample::DifferenceCoverSample(const TStr&, uint32_t, bool, bool, std::ostream&) [with TStr = SString; uint32_t = unsigned int; std::ostream = std::basic_ostream]’ diff_sample.h:461:20: 461 | _dmap(getDeltaMap(_v, _ds)), | ~~~~~~~~~~~^~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:446:13: 446 | _dc.init(new TDC(this->text(), _dcV, this->verbose(), this->sanityCheck())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:665:28: 665 | driver >(infile, infiles, outfile, false, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:391:16: warning: variable ‘amapEnts’ set but not used [-Wunused-but-set-variable=] 391 | size_t amapEnts = 1; | ^~~~~~~~ diff_sample.h: In instantiation of ‘void DifferenceCoverSample::buildSPrime(EList&, size_t) [with TStr = SString; size_t = long unsigned int]’: required from ‘void DifferenceCoverSample::build(thread_pool&, int) [with TStr = SString]’ diff_sample.h:758:2: 758 | buildSPrime(sPrime, padding); | ^~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:447:20: 447 | _dc.get()->build(_pool, this->_nthreads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:665:28: 665 | driver >(infile, infiles, outfile, false, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:645:20: warning: variable ‘added’ set but not used [-Wunused-but-set-variable=] 645 | TIndexOffU added = 0; | ^~~~~ diff_sample.h: In instantiation of ‘void DifferenceCoverSample::doBuiltSanityCheck() const [with TStr = SString]’: required from ‘void DifferenceCoverSample::build(thread_pool&, int) [with TStr = SString]’ diff_sample.h:908:26: 908 | if(this->sanityCheck()) doBuiltSanityCheck(); | ^~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:447:20: 447 | _dc.get()->build(_pool, this->_nthreads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:665:28: 665 | driver >(infile, infiles, outfile, false, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:574:20: warning: variable ‘added’ set but not used [-Wunused-but-set-variable=] 574 | TIndexOffU added = 0; | ^~~~~ diff_sample.h: In instantiation of ‘void DifferenceCoverSample::buildSPrime(EList&, size_t) [with TStr = S2bDnaString; size_t = long unsigned int]’: required from ‘void DifferenceCoverSample::build(thread_pool&, int) [with TStr = S2bDnaString]’ diff_sample.h:758:2: 758 | buildSPrime(sPrime, padding); | ^~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = S2bDnaString]’ blockwise_sa.h:447:20: 447 | _dc.get()->build(_pool, this->_nthreads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = S2bDnaString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:676:25: 676 | driver(infile, infiles, outfile, true, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:645:20: warning: variable ‘added’ set but not used [-Wunused-but-set-variable=] 645 | TIndexOffU added = 0; | ^~~~~ diff_sample.h: In instantiation of ‘void DifferenceCoverSample::doBuiltSanityCheck() const [with TStr = S2bDnaString]’: required from ‘void DifferenceCoverSample::build(thread_pool&, int) [with TStr = S2bDnaString]’ diff_sample.h:908:26: 908 | if(this->sanityCheck()) doBuiltSanityCheck(); | ^~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = S2bDnaString]’ blockwise_sa.h:447:20: 447 | _dc.get()->build(_pool, this->_nthreads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = S2bDnaString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:676:25: 676 | driver(infile, infiles, outfile, true, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:574:20: warning: variable ‘added’ set but not used [-Wunused-but-set-variable=] 574 | TIndexOffU added = 0; | ^~~~~ In file included from bt2_idx.h:46: In function ‘fastaRefReadAppend(FileBuf&, bool, S2bDnaString&, unsigned long&, RefReadInParams&, std::__cxx11::basic_string, std::allocator >*)RefRecord’, inlined from ‘Ebwt::joinToDisk(EList&, EList&, unsigned long, RefReadInParams const&, S2bDnaString&, std::basic_ostream >&, std::basic_ostream >&)void [clone .isra.0]’ at bt2_idx.h:2741:38: ref_read.h:295:49: warning: array subscript -1 is below array bounds of ‘uint8_t[]’ [-Warray-bounds=] 295 | if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A'; | ~~~~~~~~~~~~^ In file included from bt2_idx.h:39: alphabet.h: In member function ‘Ebwt::joinToDisk(EList&, EList&, unsigned long, RefReadInParams const&, S2bDnaString&, std::basic_ostream >&, std::basic_ostream >&)void [clone .isra.0]’: alphabet.h:36:16: note: while referencing ‘asc2dnacat’ 36 | extern uint8_t asc2dnacat[]; | ^~~~~~~~~~ ref_read.h: In function ‘fastaRefReadAppend >(FileBuf&, bool, SString&, unsigned long&, RefReadInParams&, std::__cxx11::basic_string, std::allocator >*)RefRecord’: ref_read.h:295:49: warning: array subscript -1 is below array bounds of ‘uint8_t[]’ [-Warray-bounds=] 295 | if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A'; | ~~~~~~~~~~~~^ alphabet.h:36:16: note: while referencing ‘asc2dnacat’ 36 | extern uint8_t asc2dnacat[]; | ^~~~~~~~~~ bt2_util.cpp: In member function ‘void Ebwt::checkOrigs(const EList >&, bool, bool) const’: bt2_util.cpp:175:20: warning: variable ‘restOff’ set but not used [-Wunused-but-set-variable=] 175 | TIndexOffU restOff = 0; | ^~~~~~~ g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-build-s bt2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp diff_sample.cpp bowtie_build_main.cpp \ -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lpthread -lz In file included from blockwise_sa.h:41, from bt2_idx.h:42, from bt2_build.cpp:28: diff_sample.h: In instantiation of ‘EList getDeltaMap(T, const EList&) [with T = unsigned int]’: required from ‘DifferenceCoverSample::DifferenceCoverSample(const TStr&, uint32_t, bool, bool, std::ostream&) [with TStr = SString; uint32_t = unsigned int; std::ostream = std::basic_ostream]’ diff_sample.h:461:20: 461 | _dmap(getDeltaMap(_v, _ds)), | ~~~~~~~~~~~^~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:446:13: 446 | _dc.init(new TDC(this->text(), _dcV, this->verbose(), this->sanityCheck())); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:665:28: 665 | driver >(infile, infiles, outfile, false, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:391:16: warning: variable ‘amapEnts’ set but not used [-Wunused-but-set-variable=] 391 | size_t amapEnts = 1; | ^~~~~~~~ diff_sample.h: In instantiation of ‘void DifferenceCoverSample::buildSPrime(EList&, size_t) [with TStr = SString; size_t = long unsigned int]’: required from ‘void DifferenceCoverSample::build(thread_pool&, int) [with TStr = SString]’ diff_sample.h:758:2: 758 | buildSPrime(sPrime, padding); | ^~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:447:20: 447 | _dc.get()->build(_pool, this->_nthreads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:665:28: 665 | driver >(infile, infiles, outfile, false, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:645:20: warning: variable ‘added’ set but not used [-Wunused-but-set-variable=] 645 | TIndexOffU added = 0; | ^~~~~ diff_sample.h: In instantiation of ‘void DifferenceCoverSample::doBuiltSanityCheck() const [with TStr = SString]’: required from ‘void DifferenceCoverSample::build(thread_pool&, int) [with TStr = SString]’ diff_sample.h:908:26: 908 | if(this->sanityCheck()) doBuiltSanityCheck(); | ^~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:447:20: 447 | _dc.get()->build(_pool, this->_nthreads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:665:28: 665 | driver >(infile, infiles, outfile, false, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:574:20: warning: variable ‘added’ set but not used [-Wunused-but-set-variable=] 574 | TIndexOffU added = 0; | ^~~~~ diff_sample.h: In instantiation of ‘void DifferenceCoverSample::buildSPrime(EList&, size_t) [with TStr = S2bDnaString; size_t = long unsigned int]’: required from ‘void DifferenceCoverSample::build(thread_pool&, int) [with TStr = S2bDnaString]’ diff_sample.h:758:2: 758 | buildSPrime(sPrime, padding); | ^~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = S2bDnaString]’ blockwise_sa.h:447:20: 447 | _dc.get()->build(_pool, this->_nthreads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = S2bDnaString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:676:25: 676 | driver(infile, infiles, outfile, true, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:645:20: warning: variable ‘added’ set but not used [-Wunused-but-set-variable=] 645 | TIndexOffU added = 0; | ^~~~~ diff_sample.h: In instantiation of ‘void DifferenceCoverSample::doBuiltSanityCheck() const [with TStr = S2bDnaString]’: required from ‘void DifferenceCoverSample::build(thread_pool&, int) [with TStr = S2bDnaString]’ diff_sample.h:908:26: 908 | if(this->sanityCheck()) doBuiltSanityCheck(); | ^~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::build() [with TStr = S2bDnaString]’ blockwise_sa.h:447:20: 447 | _dc.get()->build(_pool, this->_nthreads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = S2bDnaString]’ blockwise_sa.h:426:4: 426 | build(); | ^~~~~ required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, thread_pool&, 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]’ blockwise_sa.h:275:30: 275 | { _randomSrc.init(__seed); reset(); } | ^~~~~ 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:1142:34: 1142 | KarkkainenBlockwiseSA bsa(s, bmax, nthreads, pool, dcv, seed, _sanity, _passMemExc, _verbose, outfile); | ^~~ 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_idx.h:711:23: 711 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 712 | is, | ~~~ 713 | szs, | ~~~~ 714 | sztot, | ~~~~~~ 715 | refparams, | ~~~~~~~~~~ 716 | fout1, | ~~~~~~ 717 | fout2, | ~~~~~~ 718 | file, | ~~~~~ 719 | saOut, | ~~~~~~ 720 | bwtOut, | ~~~~~~~ 721 | nthreads, | ~~~~~~~~~ 722 | useBlockwise, | ~~~~~~~~~~~~~ 723 | bmax, | ~~~~~ 724 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 725 | bmaxDivN, | ~~~~~~~~~ 726 | dcv, | ~~~~ 727 | seed, | ~~~~~ 728 | verbose); | ~~~~~~~~ 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:477:7: 477 | Ebwt ebwt( | ^~~~ required from here bt2_build.cpp:676:25: 676 | driver(infile, infiles, outfile, true, REF_READ_FORWARD); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:574:20: warning: variable ‘added’ set but not used [-Wunused-but-set-variable=] 574 | TIndexOffU added = 0; | ^~~~~ In file included from bt2_idx.h:46: In function ‘fastaRefReadAppend(FileBuf&, bool, S2bDnaString&, unsigned int&, RefReadInParams&, std::__cxx11::basic_string, std::allocator >*)RefRecord’, inlined from ‘Ebwt::joinToDisk(EList&, EList&, unsigned int, RefReadInParams const&, S2bDnaString&, std::basic_ostream >&, std::basic_ostream >&)void [clone .isra.0]’ at bt2_idx.h:2741:38: ref_read.h:295:49: warning: array subscript -1 is below array bounds of ‘uint8_t[]’ [-Warray-bounds=] 295 | if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A'; | ~~~~~~~~~~~~^ In file included from bt2_idx.h:39: alphabet.h: In member function ‘Ebwt::joinToDisk(EList&, EList&, unsigned int, RefReadInParams const&, S2bDnaString&, std::basic_ostream >&, std::basic_ostream >&)void [clone .isra.0]’: alphabet.h:36:16: note: while referencing ‘asc2dnacat’ 36 | extern uint8_t asc2dnacat[]; | ^~~~~~~~~~ ref_read.h: In function ‘fastaRefReadAppend >(FileBuf&, bool, SString&, unsigned int&, RefReadInParams&, std::__cxx11::basic_string, std::allocator >*)RefRecord’: ref_read.h:295:49: warning: array subscript -1 is below array bounds of ‘uint8_t[]’ [-Warray-bounds=] 295 | if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A'; | ~~~~~~~~~~~~^ alphabet.h:36:16: note: while referencing ‘asc2dnacat’ 36 | extern uint8_t asc2dnacat[]; | ^~~~~~~~~~ bt2_util.cpp: In member function ‘void Ebwt::checkOrigs(const EList >&, bool, bool) const’: bt2_util.cpp:175:20: warning: variable ‘restOff’ set but not used [-Wunused-but-set-variable=] 175 | TIndexOffU restOff = 0; | ^~~~~~~ g++ -O3 -funroll-loops -g3 \ -DCOMPILER_OPTIONS="\"-O3 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \ -Ithird_party \ -o bowtie2-inspect-l bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lpthread -lz g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-align-s bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lpthread -lz In file included from aligner_driver.h:78, from bt2_search.cpp:53: aligner_seed2.h: In member function ‘void Descent::collectEdits(EList&, const Edit*, EFactory&)’: aligner_seed2.h:1264:24: warning: variable ‘nuninited’ set but not used [-Wunused-but-set-variable=] 1264 | size_t nuninited = 0; | ^~~~~~~~~ aligner_seed2.h: In member function ‘bool DescentPartialAlignmentSelector::nextPartial(const DescentDriver&, const Ebwt&, const BitPairReference&, RandomSource&, AlnRes&, WalkMetrics&, PerReadMetrics&)’: aligner_seed2.h:2448:24: warning: variable ‘ns’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~ aligner_seed2.h:2448:32: warning: variable ‘ngap’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~ aligner_seed2.h:2448:42: warning: variable ‘nrefn’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~~ In file included from aligner_sw.h:75, from bt2_search.cpp:54: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ bt2_search.cpp: In instantiation of ‘void thread_monitor(int, int, EList&, EList&) [with T = std::thread]’: required from here bt2_search.cpp:4767:18: 4767 | thread_monitor(pid, orig_threads, tids, threads); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bt2_search.cpp:4642:13: warning: variable ‘steal_ctr’ set but not used [-Wunused-but-set-variable=] 4642 | int steal_ctr = 1; | ^~~~~~~~~ In file included from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:27, from blockwise_sa.h:41, from bt2_idx.h:42, from bt2_search.cpp:41: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ bt2_search.cpp: In function ‘read_dir(char const*, int*)’: bt2_search.cpp:4607:67: warning: pointer ‘dir_31’ may be used after ‘closedir’ [-Wuse-after-free] 4607 | cerr << "read_dir: could not close directory " << dir << endl; | ^~~ bt2_search.cpp:4605:20: note: call to ‘closedir’ here 4605 | if(closedir(dir) != 0) { | ~~~~~~~~^~~~~ In file included from /usr/include/c++/16/ostream:42, from /usr/include/c++/16/istream:43, from /usr/include/c++/16/fstream:42, from bt2_search.cpp:22: In member function ‘std::basic_ostream >::operator<<(void const*)’, inlined from ‘read_dir(char const*, int*)’ at bt2_search.cpp:4607:53, inlined from ‘steal_threads(int, int, EList&, EList&)void’ at bt2_search.cpp:4623:27, inlined from ‘thread_monitor(int, int, EList&, EList&)void’ at bt2_search.cpp:4644:16, inlined from ‘multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4767:18: /usr/include/c++/16/bits/ostream.h:302:25: warning: pointer may be used after ‘closedir’ [-Wuse-after-free] 302 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function ‘read_dir(char const*, int*)’, inlined from ‘steal_threads(int, int, EList&, EList&)void’ at bt2_search.cpp:4623:27, inlined from ‘thread_monitor(int, int, EList&, EList&)void’ at bt2_search.cpp:4644:16, inlined from ‘multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4767:18: bt2_search.cpp:4605:20: note: call to ‘closedir’ here 4605 | if(closedir(dir) != 0) { | ~~~~~~~~^~~~~ bt2_util.cpp: In member function ‘void Ebwt::checkOrigs(const EList >&, bool, bool) const’: bt2_util.cpp:175:20: warning: variable ‘restOff’ set but not used [-Wunused-but-set-variable=] 175 | TIndexOffU restOff = 0; | ^~~~~~~ In file included from aligner_cache.h:59, from aligner_seed.cpp:21: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_seed2.cpp:22: aligner_seed2.h: In member function ‘void Descent::collectEdits(EList&, const Edit*, EFactory&)’: aligner_seed2.h:1264:24: warning: variable ‘nuninited’ set but not used [-Wunused-but-set-variable=] 1264 | size_t nuninited = 0; | ^~~~~~~~~ aligner_seed2.h: In member function ‘bool DescentPartialAlignmentSelector::nextPartial(const DescentDriver&, const Ebwt&, const BitPairReference&, RandomSource&, AlnRes&, WalkMetrics&, PerReadMetrics&)’: aligner_seed2.h:2448:24: warning: variable ‘ns’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~ aligner_seed2.h:2448:32: warning: variable ‘ngap’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~ aligner_seed2.h:2448:42: warning: variable ‘nrefn’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~~ aligner_seed2.cpp: In member function ‘bool Descent::followMatches(const Read&, const Scoring&, const Ebwt&, const Ebwt&, DescentRedundancyChecker&, EFactory&, EFactory&, const EList&, const EList&, EHeap >&, DescentAlignmentSink&, DescentMetrics&, PerReadMetrics&, bool&, bool&, bool&, TReadOff&, TIndexOffU&, TIndexOffU&, TIndexOffU&, TIndexOffU&)’: aligner_seed2.cpp:1646:32: warning: variable ‘nopts’ set but not used [-Wunused-but-set-variable=] 1646 | size_t nopts = 0; | ^~~~~ aligner_seed2.cpp:1383:16: warning: variable ‘off3p’ set but not used [-Wunused-but-set-variable=] 1383 | size_t off3p = q.length() - off5p - 1; | ^~~~~ aligner_seed2.cpp:1390:16: warning: variable ‘nalloc’ set but not used [-Wunused-but-set-variable=] 1390 | size_t nalloc = 0; | ^~~~~~ In file included from aligner_sw.h:75, from aligner_sw.cpp:25: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_sw.h:75, from aligner_sw_driver.h:81, from aligner_sw_driver.cpp:47: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ aligner_sw_driver.cpp: In member function ‘int SwDriver::extendSeeds(Read&, bool, SeedResults&, const Ebwt&, const Ebwt*, const BitPairReference&, SwAligner&, const Scoring&, int, int, int, TAlScore&, int, size_t, bool, size_t, size_t, size_t, size_t, size_t, bool, bool, size_t, size_t, bool, int, AlignmentCacheIface&, RandomSource&, WalkMetrics&, SwMetrics&, PerReadMetrics&, AlnSinkWrap*, bool, bool&)’: aligner_sw_driver.cpp:901:32: warning: variable ‘riter’ set but not used [-Wunused-but-set-variable=] 901 | size_t riter = 0; | ^~~~~ aligner_sw_driver.cpp:823:16: warning: variable ‘eltsDone’ set but not used [-Wunused-but-set-variable=] 823 | size_t eltsDone = 0; | ^~~~~~~~ aligner_sw_driver.cpp: In member function ‘int SwDriver::extendSeedsPaired(Read&, Read&, bool, bool, SeedResults&, const Ebwt&, const Ebwt*, const BitPairReference&, SwAligner&, SwAligner&, const Scoring&, const PairedEndPolicy&, int, int, int, TAlScore&, TAlScore&, int, int, bool, bool, size_t, bool, size_t, size_t, size_t, size_t, size_t, size_t, size_t, bool, bool, size_t, size_t, bool, int, AlignmentCacheIface&, RandomSource&, WalkMetrics&, SwMetrics&, SwMetrics&, PerReadMetrics&, AlnSinkWrap*, bool, bool, bool, bool, bool&)’: aligner_sw_driver.cpp:1504:16: warning: variable ‘eltsDone’ set but not used [-Wunused-but-set-variable=] 1504 | size_t eltsDone = 0; | ^~~~~~~~ In file included from aligner_cache.h:59, from aligner_sw_driver.cpp:46: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_cache.h:59, from aligner_cache.cpp:22: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = SAVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = SAVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.cpp:81:24: 81 | SANode *s = samap_.add(pool(), sak, &added); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from read.h:25, from aln_sink.h:24, from aln_sink.cpp:22: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ aligner_bt.cpp: In member function ‘void BtBranchTracer::triangleFill(int64_t, int64_t, int, TAlScore, TAlScore, RandomSource&, int64_t&, int64_t&, int&, TAlScore&, bool&, bool&)’: aligner_bt.cpp:126:24: warning: variable ‘neval’ set but not used [-Wunused-but-set-variable=] 126 | size_t neval = 0; // # cells evaluated in this diag | ^~~~~ aligner_bt.cpp: In member function ‘void BtBranch::init(const BtBranchProblem&, size_t, TAlScore, TAlScore, int64_t, int64_t, Edit, int, bool, bool)’: aligner_bt.cpp:1171:16: warning: variable ‘iters’ set but not used [-Wunused-but-set-variable=] 1171 | size_t iters = 0; | ^~~~~ In file included from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from sse_wrap.h:116, from aligner_sw.h:73: aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherLoc16(int&, bool)’: aligner_swsse_loc_i16.cpp:479:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 479 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:479:22: note: in expansion of macro ‘sse_slli_epi16’ 479 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ^~~~~~~~~~~~~~ aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesLocalSseI16(int&, bool)’: aligner_swsse_loc_i16.cpp:1084:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 1084 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:1084:22: note: in expansion of macro ‘sse_slli_epi16’ 1084 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ^~~~~~~~~~~~~~ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from sse_wrap.h:116, from aligner_sw.h:73: aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherEE16(int&, bool)’: aligner_swsse_ee_i16.cpp:467:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 467 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:467:22: note: in expansion of macro ‘sse_slli_epi16’ 467 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ^~~~~~~~~~~~~~ aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesEnd2EndSseI16(int&, bool)’: aligner_swsse_ee_i16.cpp:936:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 936 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:936:22: note: in expansion of macro ‘sse_slli_epi16’ 936 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ^~~~~~~~~~~~~~ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_driver.h:78, from aligner_driver.cpp:20: aligner_seed2.h: In member function ‘void Descent::collectEdits(EList&, const Edit*, EFactory&)’: aligner_seed2.h:1264:24: warning: variable ‘nuninited’ set but not used [-Wunused-but-set-variable=] 1264 | size_t nuninited = 0; | ^~~~~~~~~ aligner_seed2.h: In member function ‘bool DescentPartialAlignmentSelector::nextPartial(const DescentDriver&, const Ebwt&, const BitPairReference&, RandomSource&, AlnRes&, WalkMetrics&, PerReadMetrics&)’: aligner_seed2.h:2448:24: warning: variable ‘ns’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~ aligner_seed2.h:2448:32: warning: variable ‘ngap’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~ aligner_seed2.h:2448:42: warning: variable ‘nrefn’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~~ g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -Ithird_party \ -o bowtie2-align-l bt2_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \ -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lpthread -lz In file included from aligner_driver.h:78, from bt2_search.cpp:53: aligner_seed2.h: In member function ‘void Descent::collectEdits(EList&, const Edit*, EFactory&)’: aligner_seed2.h:1264:24: warning: variable ‘nuninited’ set but not used [-Wunused-but-set-variable=] 1264 | size_t nuninited = 0; | ^~~~~~~~~ aligner_seed2.h: In member function ‘bool DescentPartialAlignmentSelector::nextPartial(const DescentDriver&, const Ebwt&, const BitPairReference&, RandomSource&, AlnRes&, WalkMetrics&, PerReadMetrics&)’: aligner_seed2.h:2448:24: warning: variable ‘ns’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~ aligner_seed2.h:2448:32: warning: variable ‘ngap’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~ aligner_seed2.h:2448:42: warning: variable ‘nrefn’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~~ In file included from aligner_sw.h:75, from bt2_search.cpp:54: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ bt2_search.cpp: In instantiation of ‘void thread_monitor(int, int, EList&, EList&) [with T = std::thread]’: required from here bt2_search.cpp:4767:18: 4767 | thread_monitor(pid, orig_threads, tids, threads); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bt2_search.cpp:4642:13: warning: variable ‘steal_ctr’ set but not used [-Wunused-but-set-variable=] 4642 | int steal_ctr = 1; | ^~~~~~~~~ In file included from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:27, from blockwise_sa.h:41, from bt2_idx.h:42, from bt2_search.cpp:41: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ bt2_search.cpp: In function ‘read_dir(char const*, int*)’: bt2_search.cpp:4607:67: warning: pointer ‘dir_31’ may be used after ‘closedir’ [-Wuse-after-free] 4607 | cerr << "read_dir: could not close directory " << dir << endl; | ^~~ bt2_search.cpp:4605:20: note: call to ‘closedir’ here 4605 | if(closedir(dir) != 0) { | ~~~~~~~~^~~~~ In file included from /usr/include/c++/16/ostream:42, from /usr/include/c++/16/istream:43, from /usr/include/c++/16/fstream:42, from bt2_search.cpp:22: In member function ‘std::basic_ostream >::operator<<(void const*)’, inlined from ‘read_dir(char const*, int*)’ at bt2_search.cpp:4607:53, inlined from ‘steal_threads(int, int, EList&, EList&)void’ at bt2_search.cpp:4623:27, inlined from ‘thread_monitor(int, int, EList&, EList&)void’ at bt2_search.cpp:4644:16, inlined from ‘multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4767:18: /usr/include/c++/16/bits/ostream.h:302:25: warning: pointer may be used after ‘closedir’ [-Wuse-after-free] 302 | { return _M_insert(__p); } | ~~~~~~~~~^~~~~ In function ‘read_dir(char const*, int*)’, inlined from ‘steal_threads(int, int, EList&, EList&)void’ at bt2_search.cpp:4623:27, inlined from ‘thread_monitor(int, int, EList&, EList&)void’ at bt2_search.cpp:4644:16, inlined from ‘multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)’ at bt2_search.cpp:4767:18: bt2_search.cpp:4605:20: note: call to ‘closedir’ here 4605 | if(closedir(dir) != 0) { | ~~~~~~~~^~~~~ bt2_util.cpp: In member function ‘void Ebwt::checkOrigs(const EList >&, bool, bool) const’: bt2_util.cpp:175:20: warning: variable ‘restOff’ set but not used [-Wunused-but-set-variable=] 175 | TIndexOffU restOff = 0; | ^~~~~~~ In file included from aligner_cache.h:59, from aligner_seed.cpp:21: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_seed2.cpp:22: aligner_seed2.h: In member function ‘void Descent::collectEdits(EList&, const Edit*, EFactory&)’: aligner_seed2.h:1264:24: warning: variable ‘nuninited’ set but not used [-Wunused-but-set-variable=] 1264 | size_t nuninited = 0; | ^~~~~~~~~ aligner_seed2.h: In member function ‘bool DescentPartialAlignmentSelector::nextPartial(const DescentDriver&, const Ebwt&, const BitPairReference&, RandomSource&, AlnRes&, WalkMetrics&, PerReadMetrics&)’: aligner_seed2.h:2448:24: warning: variable ‘ns’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~ aligner_seed2.h:2448:32: warning: variable ‘ngap’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~ aligner_seed2.h:2448:42: warning: variable ‘nrefn’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~~ aligner_seed2.cpp: In member function ‘bool Descent::followMatches(const Read&, const Scoring&, const Ebwt&, const Ebwt&, DescentRedundancyChecker&, EFactory&, EFactory&, const EList&, const EList&, EHeap >&, DescentAlignmentSink&, DescentMetrics&, PerReadMetrics&, bool&, bool&, bool&, TReadOff&, TIndexOffU&, TIndexOffU&, TIndexOffU&, TIndexOffU&)’: aligner_seed2.cpp:1646:32: warning: variable ‘nopts’ set but not used [-Wunused-but-set-variable=] 1646 | size_t nopts = 0; | ^~~~~ aligner_seed2.cpp:1383:16: warning: variable ‘off3p’ set but not used [-Wunused-but-set-variable=] 1383 | size_t off3p = q.length() - off5p - 1; | ^~~~~ aligner_seed2.cpp:1390:16: warning: variable ‘nalloc’ set but not used [-Wunused-but-set-variable=] 1390 | size_t nalloc = 0; | ^~~~~~ In file included from aligner_sw.h:75, from aligner_sw.cpp:25: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_sw.h:75, from aligner_sw_driver.h:81, from aligner_sw_driver.cpp:47: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ aligner_sw_driver.cpp: In member function ‘int SwDriver::extendSeeds(Read&, bool, SeedResults&, const Ebwt&, const Ebwt*, const BitPairReference&, SwAligner&, const Scoring&, int, int, int, TAlScore&, int, size_t, bool, size_t, size_t, size_t, size_t, size_t, bool, bool, size_t, size_t, bool, int, AlignmentCacheIface&, RandomSource&, WalkMetrics&, SwMetrics&, PerReadMetrics&, AlnSinkWrap*, bool, bool&)’: aligner_sw_driver.cpp:901:32: warning: variable ‘riter’ set but not used [-Wunused-but-set-variable=] 901 | size_t riter = 0; | ^~~~~ aligner_sw_driver.cpp:823:16: warning: variable ‘eltsDone’ set but not used [-Wunused-but-set-variable=] 823 | size_t eltsDone = 0; | ^~~~~~~~ aligner_sw_driver.cpp: In member function ‘int SwDriver::extendSeedsPaired(Read&, Read&, bool, bool, SeedResults&, const Ebwt&, const Ebwt*, const BitPairReference&, SwAligner&, SwAligner&, const Scoring&, const PairedEndPolicy&, int, int, int, TAlScore&, TAlScore&, int, int, bool, bool, size_t, bool, size_t, size_t, size_t, size_t, size_t, size_t, size_t, bool, bool, size_t, size_t, bool, int, AlignmentCacheIface&, RandomSource&, WalkMetrics&, SwMetrics&, SwMetrics&, PerReadMetrics&, AlnSinkWrap*, bool, bool, bool, bool, bool&)’: aligner_sw_driver.cpp:1504:16: warning: variable ‘eltsDone’ set but not used [-Wunused-but-set-variable=] 1504 | size_t eltsDone = 0; | ^~~~~~~~ In file included from aligner_cache.h:59, from aligner_sw_driver.cpp:46: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_cache.h:59, from aligner_cache.cpp:22: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = SAVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = SAVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.cpp:81:24: 81 | SANode *s = samap_.add(pool(), sak, &added); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from read.h:25, from aln_sink.h:24, from aln_sink.cpp:22: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ aligner_bt.cpp: In member function ‘void BtBranchTracer::triangleFill(int64_t, int64_t, int, TAlScore, TAlScore, RandomSource&, int64_t&, int64_t&, int&, TAlScore&, bool&, bool&)’: aligner_bt.cpp:126:24: warning: variable ‘neval’ set but not used [-Wunused-but-set-variable=] 126 | size_t neval = 0; // # cells evaluated in this diag | ^~~~~ aligner_bt.cpp: In member function ‘void BtBranch::init(const BtBranchProblem&, size_t, TAlScore, TAlScore, int64_t, int64_t, Edit, int, bool, bool)’: aligner_bt.cpp:1171:16: warning: variable ‘iters’ set but not used [-Wunused-but-set-variable=] 1171 | size_t iters = 0; | ^~~~~ In file included from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from sse_wrap.h:116, from aligner_sw.h:73: aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherLoc16(int&, bool)’: aligner_swsse_loc_i16.cpp:479:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 479 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:479:22: note: in expansion of macro ‘sse_slli_epi16’ 479 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ^~~~~~~~~~~~~~ aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesLocalSseI16(int&, bool)’: aligner_swsse_loc_i16.cpp:1084:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 1084 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:1084:22: note: in expansion of macro ‘sse_slli_epi16’ 1084 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ^~~~~~~~~~~~~~ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_sw.h:75, from aligner_swsse_ee_i16.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from sse_wrap.h:116, from aligner_sw.h:73: aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherEE16(int&, bool)’: aligner_swsse_ee_i16.cpp:467:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 467 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:467:22: note: in expansion of macro ‘sse_slli_epi16’ 467 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ^~~~~~~~~~~~~~ aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesEnd2EndSseI16(int&, bool)’: aligner_swsse_ee_i16.cpp:936:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 936 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:936:22: note: in expansion of macro ‘sse_slli_epi16’ 936 | vf = sse_slli_epi16(vf, NBITS_PER_WORD-1); | ^~~~~~~~~~~~~~ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ In file included from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74: ds.h: In instantiation of ‘void RedBlack::addNode(TNode*, TNode*, bool) [with K = QKey; P = QVal; TNode = RedBlackNode]’: required from ‘RedBlack::TNode* RedBlack::add(Pool&, const K&, bool*) [with K = QKey; P = QVal; TNode = RedBlackNode]’ ds.h:3844:11: 3844 | addNode(cur, parent, leftChild); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ required from here aligner_cache.h:690:23: 690 | QNode *n = qmap_.add(pool(), qk, added); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~ ds.h:4078:29: warning: variable ‘thru’ set but not used [-Wunused-but-set-variable=] 4078 | int thru = 0; | ^~~~ In file included from aligner_driver.h:78, from aligner_driver.cpp:20: aligner_seed2.h: In member function ‘void Descent::collectEdits(EList&, const Edit*, EFactory&)’: aligner_seed2.h:1264:24: warning: variable ‘nuninited’ set but not used [-Wunused-but-set-variable=] 1264 | size_t nuninited = 0; | ^~~~~~~~~ aligner_seed2.h: In member function ‘bool DescentPartialAlignmentSelector::nextPartial(const DescentDriver&, const Ebwt&, const BitPairReference&, RandomSource&, AlnRes&, WalkMetrics&, PerReadMetrics&)’: aligner_seed2.h:2448:24: warning: variable ‘ns’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~ aligner_seed2.h:2448:32: warning: variable ‘ngap’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~ aligner_seed2.h:2448:42: warning: variable ‘nrefn’ set but not used [-Wunused-but-set-variable=] 2448 | size_t ns = 0, ngap = 0, nrefn = 0; | ^~~~~ + RPM_EC=0 ++ jobs -p + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.V4lNcS + umask 022 + cd /builddir/build/BUILD/bowtie2-2.5.1-build + '[' /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT ++ dirname /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT + mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build + mkdir /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bowtie2-2.5.1 + /usr/bin/make install DESTDIR=/builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT 'INSTALL=/usr/bin/install -p' PREFIX=/usr mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \ cp -f $file /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin ; \ done + mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/man/man1 + for cmd in bowtie2 bowtie2-{build,inspect} + help2man -N -s 1 -o /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/man/man1/bowtie2.1 --version-string=2.5.1 /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin/bowtie2 + for cmd in bowtie2 bowtie2-{build,inspect} + help2man -N -s 1 -o /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/man/man1/bowtie2-build.1 --version-string=2.5.1 /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin/bowtie2-build + for cmd in bowtie2 bowtie2-{build,inspect} + help2man -N -s 1 -o /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/man/man1/bowtie2-inspect.1 --version-string=2.5.1 /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/bin/bowtie2-inspect + /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 2.5.1-7.fc44 --unique-debug-suffix -2.5.1-7.fc44.ppc64le --unique-debug-src-base bowtie2-2.5.1-7.fc44.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1 find-debuginfo: starting Extracting debug info from 6 files DWARF-compressing 6 files sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/bowtie2-2.5.1-7.fc44.ppc64le find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + COMPRESS='gzip -9 -n' + COMPRESS_EXT=.gz + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j5 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j5 /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT Scanned 14 directories and 137 files, processed 3 inodes, 0 modified (0 replaced + 0 rewritten), 0 unsupported format, 0 errors + /usr/bin/linkdupes --brp /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr Scanned 13 directories and 137 files, considered 137 files, read 0 files, linked 0 files, 0 errors sum of sizes of linked files: 0 bytes Reading /builddir/build/BUILD/bowtie2-2.5.1-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.xbdyPl + umask 022 + cd /builddir/build/BUILD/bowtie2-2.5.1-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + 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 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd bowtie2-2.5.1 + for cmd in bowtie2 bowtie2-{build,inspect} + grep 'version 2.5.1' + ./bowtie2 --version /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s version 2.5.1 + for cmd in bowtie2 bowtie2-{build,inspect} + ./bowtie2-build --version + grep 'version 2.5.1' /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-build-s version 2.5.1 + for cmd in bowtie2 bowtie2-{build,inspect} + ./bowtie2-inspect --version + grep 'version 2.5.1' /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-inspect-s version 2.5.1 + sed -i '/my $binary_type/ s/"release", "debug", "sanitized"/"release"/' scripts/test/simple_tests.pl + ASAN_OPTIONS=halt_on_error=1 + UBSAN_OPTIONS=halt_on_error=1 + scripts/test/simple_tests.pl --bowtie2=./bowtie2 --bowtie2-build=./bowtie2-build --compressed \1 better written as $1 at scripts/test/simple_tests.pl line 4674. \1 better written as $1 at scripts/test/simple_tests.pl line 4675. FASTA-continuous 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 -F 10,9 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --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 -F 10,9 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 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 16 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -F 10,9 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 6 -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 15 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 15 -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 1 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:12 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 1 -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 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:15 @SQ SN:1 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -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 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:15 @SQ SN:1 LN:15 @SQ SN:2 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 0 0 2 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Should account for stretch of Ns at beginning (fw:1, sam:1) References: >0 NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:34 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 0 0 0 18 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -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 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 13 -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 12 -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 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 10 -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 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 9 -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 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 3 -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 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: trim position must be either 3 or 5 Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2 [options]* -x {-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 --sam-append-comment Append FASTA/FASTQ comment to SAM record 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/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 15 -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 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: the number bases to trim must be at least 0 Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2 [options]* -x {-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 --sam-append-comment Append FASTA/FASTQ comment to SAM record 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/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII Cline 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 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 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Cline 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -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 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Cline multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -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 2 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -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 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 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 5 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --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 --quiet -a --reads-per-batch 3 -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 11 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) Fastq 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -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 7 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 7 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 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 3 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Fastq paired 2 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA ./bowtie2 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 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 Fastq paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA ./bowtie2 -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 13 -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 15 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -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 14 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 Fasta 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz Error: reads file does not look like a FASTA file terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) Fasta 6 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 13 -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 9 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 9 -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 10 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 10 -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 5 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -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 8 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 12 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --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 Fasta multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -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 8 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -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 4 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -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 15 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -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 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 7 -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 16 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -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 5 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -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 6 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -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 1 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -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 12 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 12 -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 7 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -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 12 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 3 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 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 multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --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 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 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Raw paired 2 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA ./bowtie2 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Raw paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA ./bowtie2 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -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 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 2 -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 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 12 -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 15 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --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 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Tabbed 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" Tabbed multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --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 Tabbed multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --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 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 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 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 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" 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 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -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 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 16 -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 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 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 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. ./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values. terminate called after throwing an instance of 'int' (ERR): bowtie2-align died with signal 6 (ABRT) (core dumped) Qseq 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --trim3 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -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 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -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 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 13 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --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 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" MachName_RunNum_Lane_Tile_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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 11 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 5 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 4 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1192 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 9 -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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1028 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 11 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:250 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 13 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:290 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 4 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU MD:Z 2 (fw:1, sam:1) References: >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU MD:Z 2 (fw:0, sam:1) References: >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 9 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 9 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 8 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU Local alignment 3 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU r0 256 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU Local alignment 3 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 10 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 9 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 9 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU Mate reporting order, -a (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r2 99 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP r2 147 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP Mate reporting order, -a (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA ./bowtie2 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 4 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --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 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --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 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --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-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --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 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q --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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-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 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Overlapping; no args (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP Overlapping; no args (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP Overlapping; --no-dovetail (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --no-dovetail --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 5 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-contain --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-contain (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --no-contain --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU Scoring params 1 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG ./bowtie2 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU Scoring params 2 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 3 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG ./bowtie2 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 3 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG ./bowtie2 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 6 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG ./bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --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 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -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 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c --ignore-quals (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA ./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU (fw:1, sam:1) References: >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 217 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT ./bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 89 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU XS:i 2 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA ./bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 6 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 1 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3c (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT ./bowtie2 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 8 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4a (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT ./bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4b (fw:1, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT ./bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4b (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT ./bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5a (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA ./bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 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 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 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 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 5 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 8 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 4 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 12 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 15 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 15 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 15 -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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @SQ SN:1 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 9 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @SQ SN:1 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 16 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 11 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 16 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 16 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 1 255 29S23M = 1 -68 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:-128 YT:Z:CP r0 163 0 1 255 45S15M = 1 68 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-128 XN:i:9 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:14T0 YS:i:-78 YT:Z:CP matchesRef regression 1 (fw:1, sam:1) References: >0 AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:61 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:61 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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" 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r1 99 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r1 147 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 1 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r1 83 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r1 163 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 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 -s 1 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r1 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r1 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 5 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 11 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 16 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 3 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 11 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 15 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --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 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT ./bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 13 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 11 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 11 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 2 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 2 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 16 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --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 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.k.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:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 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: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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.M.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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.M.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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --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 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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 7 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 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 --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 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: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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 11 -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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 3 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 2 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC ./bowtie2 --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 5 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 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 --local --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --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: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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 7 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2 --local --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 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.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 4 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 12 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 11 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 3 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 9 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 4 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 13 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 13 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 2 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 13 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 11 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -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 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 12 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 10 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 7 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy 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 6 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 --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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --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 7 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;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 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 15 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU Gap penalties 6 (fw:0, sam:1) References: >0 ATTGTTCGTTTGTTCGTA ./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU Gap penalties 7 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i: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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA ./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 4 (fw:0, sam:1) References: >0 GAGACTTTNTACGCATCGAACTATCGCTCTA ./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 14 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU N filtering 5 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 3 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU (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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 16 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 11 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 12 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU (fw:1, sam:1) References: >0 ACNCA ./bowtie2-build --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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (1) (fw:1, sam:1) References: >0 ACNCA ./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (1) (fw:0, sam:1) References: >0 ACNCA ./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (2) (fw:1, sam:1) References: >0 ACNCANNNNNNNNCGNNNNNNNNCG ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (2) (fw:0, sam:1) References: >0 ACNCANNNNNNNNCGNNNNNNNNCG ./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU (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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 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: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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 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 --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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 15 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU (fw:1, sam:1) References: >0 ATATGCCCCATGCCCCCCTCCG ./bowtie2-build --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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:22 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:22 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 16 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" r0 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 12 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 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" 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 8 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 113 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP Simple paired-end 9 (fw:1, sam:1) References: >0 CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC ./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 2 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 2 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 8 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 12 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --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 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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 9 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --overhang --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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 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 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --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\;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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 8 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 4 -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 10 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 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 1 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 1 -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 12 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz" seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz" seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 6 (fw:1, sam:1) References: >0 AGCATCGATCAG ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index -F 10,1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:12 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 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 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 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:15 @SQ SN:1 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:15 @SQ SN:1 LN:15 @SQ SN:2 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 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 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:34 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -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 8 -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 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 2 -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 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 3 -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 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: invalid position (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --trim-to 4:12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: trim position must be either 3 or 5 Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2 [options]* -x {-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 --sam-append-comment Append FASTA/FASTQ comment to SAM record 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/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 trim-to: invalid count (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: the number bases to trim must be at least 0 Bowtie 2 version 2.5.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) Usage: bowtie2 [options]* -x {-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 --sam-append-comment Append FASTA/FASTQ comment to SAM record 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/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 Cline 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 2 -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 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 16 -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 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" Cline multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 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 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -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 14 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 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 --large-index -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -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 11 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 11 -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 11 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 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 Fastq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 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 Fastq 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 6 -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 1 -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 16 -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 15 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -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 16 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 16 -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 9 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -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 6 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -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 13 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 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 Fastq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --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 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 7 -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 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -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 1 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 3 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta 5 (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 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 7 -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 6 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -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 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 4 -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 3 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -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 15 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --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 multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 12 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 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 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -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 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Fasta paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA ./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 9 -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 8 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -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 6 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 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 4 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -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 8 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Raw multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -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 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 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 --large-index -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -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 12 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -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 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 2 (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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 10 -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 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Tabbed 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -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 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 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 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --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 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 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -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 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Tabbed paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA ./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Tabbed paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA ./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 2 -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 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Qseq 4 (fw:1, sam:1) References: >0 Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. AGCATCGATCAGTATCTGA ./bowtie2 --large-index --quiet -a --reads-per-batch 5 -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 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 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 5052. Qseq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -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 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_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 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Qseq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 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 2 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -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 13 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 10 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 12 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1192 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 4 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1028 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 6 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:250 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 1 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:290 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 5 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU MD:Z 2 (fw:0, sam:1) References: >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU MD:Z 3 (fw:1, sam:1) References: >0 CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU MD:Z 3 (fw:0, sam:1) References: >0 CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 9 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 16 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 8 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 9 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 16 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 13 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 6 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 11 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 11 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 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 --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 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 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 6 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 2 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 2 -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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 args (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --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-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --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-dovetail (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --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-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --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 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 13 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --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-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --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 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-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 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP Overlapping; --no-overlap (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 2 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG ./bowtie2 --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --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 --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --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 3,3 (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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --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 3,6 (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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -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 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 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 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --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:-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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --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:-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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 4 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 289 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --large-index --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 --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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3a (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT ./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3b (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT ./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3b (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT ./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4a (fw:1, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4a (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT ./bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --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 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 12 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 12 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 5 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 12 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 12 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 13 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --rf --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 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 --large-index --ff --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 9 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @SQ SN:1 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 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 --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @SQ SN:1 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU matchesRef regression 3 (fw:1, sam:1) References: >0 GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 14 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 6 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:61 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 12 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:61 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 9 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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" 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r1 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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 14 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 14 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 1 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 12 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 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 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 14 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 9 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 13 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 16 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 11 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 7 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 3 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 12 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --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 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 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 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU r2 16 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT ./bowtie2 --large-index --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,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" 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 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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 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" 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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" 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 4 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --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: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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 961 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 12 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 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 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2 --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --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.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 13 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 1 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 7 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 6 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 4 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -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: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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 0 316 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 13 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 15 -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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 2 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 5 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 15 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 7 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 16 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 1672 1 33M = 1738 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 1738 1 28M = 1672 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC ./bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 1738 1 28M = 1672 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 1672 1 33M = 1738 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA ./bowtie2 --large-index --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA ./bowtie2 --large-index --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 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 --large-index --local --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --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: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:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 --large-index --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 10 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2 --large-index --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 5 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 16 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 12 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --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 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 4 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 4 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 8 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 6 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 11 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 2 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 3 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 11 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 16 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 9 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 11 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=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 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 2 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy 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 10 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 12 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --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 5 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 12 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 5 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 7 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA ./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 7 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 8 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 2 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 2 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 6 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 11 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU (fw:0, sam:1) References: >0 ACNCA ./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (1) (fw:1, sam:1) References: >0 ACNCA ./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU (fw: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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 5 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 9 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 8 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 7 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:22 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU (fw:1, sam:1) References: >0 ATATGCCCCATGCCCCCCTCCG ./bowtie2 --large-index --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:22 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU Simple paired-end 13 (fw:1, sam:1) References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 7 -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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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 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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 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 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r1 131 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Simple paired-end 12 (fw:0, sam:1) References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC ./bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 113 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 115 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r1 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Simple paired-end 11 (fw:1, sam:1) References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 11 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 1 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 15 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 9 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 60 1 10M = 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 5 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 163 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 339 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 419 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 339 0 60 255 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 419 0 20 255 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Simple paired-end 2; no --no-mixed (fw:0, sam:1) References: >0 CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 153 0 4 255 10M = 4 0 ATATATATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UP r0 101 0 4 0 * = 4 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP Simple paired-end 2; --no-mixed (fw:1, sam:1) References: >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 2 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 9 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 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 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:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 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 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --large-index --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:1, sam:1) References: >0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp ./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=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 --policy SEED=0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 6 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 12 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 @PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 272 0 9 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 272 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU r0 272 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU r0 272 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU r0 272 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU PASSED + RPM_EC=0 ++ jobs -p + exit 0 Processing files: bowtie2-2.5.1-7.fc44.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.NhIh3J + umask 022 + cd /builddir/build/BUILD/bowtie2-2.5.1-build + cd bowtie2-2.5.1 + DOCDIR=/builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2 + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2 + cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/AUTHORS /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2 + cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/MANUAL /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2 + cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/MANUAL.markdown /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2 + cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/NEWS /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2 + cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/TUTORIAL /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/doc/bowtie2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.E5sCDO + umask 022 + cd /builddir/build/BUILD/bowtie2-2.5.1-build + cd bowtie2-2.5.1 + LICENSEDIR=/builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/licenses/bowtie2 + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/licenses/bowtie2 + cp -pr /builddir/build/BUILD/bowtie2-2.5.1-build/bowtie2-2.5.1/LICENSE /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT/usr/share/licenses/bowtie2 + RPM_EC=0 ++ jobs -p + exit 0 Provides: bowtie2 = 2.5.1-7.fc44 bowtie2(ppc-64) = 2.5.1-7.fc44 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_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.11)(64bit) libstdc++.so.6(CXXABI_1.3.13)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.2)(64bit) libstdc++.so.6(CXXABI_1.3.3)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.14)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.22)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) libz.so.1()(64bit) libz.so.1(ZLIB_1.2.0.2)(64bit) libz.so.1(ZLIB_1.2.3.3)(64bit) libz.so.1(ZLIB_1.2.3.5)(64bit) perl(Config) perl(File::Spec) perl(Getopt::Long) perl(POSIX) perl(Sys::Hostname) perl(strict) perl(warnings) rtld(GNU_HASH) Processing files: bowtie2-debugsource-2.5.1-7.fc44.ppc64le Provides: bowtie2-debugsource = 2.5.1-7.fc44 bowtie2-debugsource(ppc-64) = 2.5.1-7.fc44 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: bowtie2-debuginfo-2.5.1-7.fc44.ppc64le Provides: bowtie2-debuginfo = 2.5.1-7.fc44 bowtie2-debuginfo(ppc-64) = 2.5.1-7.fc44 debuginfo(build-id) = 7b5bdc154d9b68178fb9df3230dafb3deb6f04c8 debuginfo(build-id) = 80766a358cac93ac04051fc9a44b05482ca2d64d debuginfo(build-id) = 870e78a2b9f4149b5463456d9d7e7baa2049ac68 debuginfo(build-id) = 8b1f1c2a16db79e11c4ea6ab1902fb94958d12cc debuginfo(build-id) = 9ed2c0f3f93c38301725053d4ba2332d0f4f7cc8 debuginfo(build-id) = fc5343ec94b73a0fe3c4072213d6bc26be7a2e51 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: bowtie2-debugsource(ppc-64) = 2.5.1-7.fc44 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/bowtie2-2.5.1-build/BUILDROOT Wrote: /builddir/build/RPMS/bowtie2-debugsource-2.5.1-7.fc44.ppc64le.rpm Wrote: /builddir/build/RPMS/bowtie2-2.5.1-7.fc44.ppc64le.rpm Wrote: /builddir/build/RPMS/bowtie2-debuginfo-2.5.1-7.fc44.ppc64le.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.0RmWIL + umask 022 + cd /builddir/build/BUILD/bowtie2-2.5.1-build + test -d /builddir/build/BUILD/bowtie2-2.5.1-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/bowtie2-2.5.1-build + rm -rf /builddir/build/BUILD/bowtie2-2.5.1-build + RPM_EC=0 ++ jobs -p + exit 0 Finish: rpmbuild bowtie2-2.5.1-7.fc44.src.rpm Finish: build phase for bowtie2-2.5.1-7.fc44.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-ppc64le-1766674744.576197/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/bowtie2-2.5.1-7.fc44.src.rpm) Config(child) 6 minutes 0 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "bowtie2", "epoch": null, "version": "2.5.1", "release": "7.fc44", "arch": "ppc64le" }, { "name": "bowtie2", "epoch": null, "version": "2.5.1", "release": "7.fc44", "arch": "src" }, { "name": "bowtie2-debuginfo", "epoch": null, "version": "2.5.1", "release": "7.fc44", "arch": "ppc64le" }, { "name": "bowtie2-debugsource", "epoch": null, "version": "2.5.1", "release": "7.fc44", "arch": "ppc64le" } ] } RPMResults finished