Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c2a0' (ED25519) to the list of known hosts.
Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5168205 --chroot fedora-rawhide-ppc64le --detached
Version: 0.62
PID: 33109
Logging PID: 33110
Task:
{'appstream': False,
'background': True,
'build_id': 5168205,
'buildroot_pkgs': [],
'chroot': 'fedora-rawhide-ppc64le',
'enable_net': False,
'fedora_review': False,
'git_hash': 'f534a545ee5fc8efe95bc8254123bae5511e45ae',
'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/bowtie2',
'isolation': 'default',
'memory_reqs': 2048,
'package_name': 'bowtie2',
'package_version': '2.4.1-6',
'project_dirname': 'gcc-13-test',
'project_name': 'gcc-13-test',
'project_owner': 'jakub',
'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/jakub/gcc-13-test/fedora-rawhide-ppc64le/',
'id': 'copr_base',
'name': 'Copr repository'},
{'baseurl': 'https://jakub.fedorapeople.org/fedora-gcc13-$arch/',
'id': 'https_jakub_fedorapeople_org_fedora_gcc13_arch',
'name': 'Additional repo https_jakub_fedorapeople_org_fedora_gcc13_arch'}],
'sandbox': 'jakub/gcc-13-test--jakub',
'source_json': {},
'source_type': None,
'submitter': 'jakub',
'tags': [],
'task_id': '5168205-fedora-rawhide-ppc64le',
'timeout': 115200,
'uses_devel_repo': False,
'with_opts': [],
'without_opts': []}
Running: git clone https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/bowtie2 /var/lib/copr-rpmbuild/workspace/workdir-1iufpb2a/bowtie2 --depth 500 --no-single-branch --recursive
cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/jakub/gcc-13-test/bowtie2', '/var/lib/copr-rpmbuild/workspace/workdir-1iufpb2a/bowtie2', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout:
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-1iufpb2a/bowtie2'...
Running: git checkout f534a545ee5fc8efe95bc8254123bae5511e45ae
cmd: ['git', 'checkout', 'f534a545ee5fc8efe95bc8254123bae5511e45ae']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-1iufpb2a/bowtie2
rc: 0
stdout:
stderr: Note: switching to 'f534a545ee5fc8efe95bc8254123bae5511e45ae'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:
git switch -c <new-branch-name>
Or undo this operation with:
git switch -
Turn off this advice by setting config variable advice.detachedHead to false
HEAD is now at f534a54 automatic import of bowtie2
Running: copr-distgit-client sources
cmd: ['copr-distgit-client', 'sources']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-1iufpb2a/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
/usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated
INFO: Downloading v2.4.1.tar.gz
INFO: Calling: curl -H Pragma: -o v2.4.1.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jakub/gcc-13-test/bowtie2/v2.4.1.tar.gz/md5/5938482fab363c6356f9662cce38f99c/v2.4.1.tar.gz
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 10.0M 100 10.0M 0 0 17.7M 0 --:--:-- --:--:-- --:--:-- 17.7M
INFO: Reading stdout from command: md5sum v2.4.1.tar.gz
Running (timeout=115200): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-1iufpb2a/bowtie2/bowtie2.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-1iufpb2a/bowtie2 --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1671784311.816071 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-1iufpb2a/bowtie2/bowtie2.spec) Config(fedora-rawhide-ppc64le)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1671784311.816071/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start(bootstrap): dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Updating Subscription Management repositories.
Unable to read consumer identity
This system is not registered with an entitlement server. You can use subscription-manager to register.
Copr repository 11 MB/s | 4.1 MB 00:00
Additional repo https_jakub_fedorapeople_org_fe 235 kB/s | 84 kB 00:00
fedora 20 MB/s | 60 MB 00:02
Dependencies resolved.
==========================================================================================================================
Package Arch Version Repository Size
==========================================================================================================================
Installing:
dnf noarch 4.14.0-1.fc38 fedora 480 k
dnf-plugins-core noarch 4.3.1-1.fc38 fedora 34 k
Installing dependencies:
alternatives ppc64le 1.21-1.fc38 fedora 40 k
audit-libs ppc64le 3.0.9-1.fc38 copr_base 131 k
basesystem noarch 11-14.fc37 fedora 7.0 k
bash ppc64le 5.2.9-3.fc38 copr_base 1.9 M
bzip2-libs ppc64le 1.0.8-12.fc37 fedora 47 k
ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k
coreutils ppc64le 9.1-8.fc38 fedora 1.4 M
coreutils-common ppc64le 9.1-8.fc38 fedora 2.0 M
crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k
curl ppc64le 7.87.0-1.fc38 fedora 348 k
cyrus-sasl-lib ppc64le 2.1.28-8.fc38 fedora 881 k
dbus-libs ppc64le 1:1.14.4-1.fc38 fedora 176 k
dnf-data noarch 4.14.0-1.fc38 fedora 43 k
elfutils-default-yama-scope noarch 0.188-3.fc38 fedora 15 k
elfutils-libelf ppc64le 0.188-3.fc38 fedora 205 k
elfutils-libs ppc64le 0.188-3.fc38 fedora 291 k
expat ppc64le 2.5.0-1.fc38 fedora 117 k
fedora-gpg-keys noarch 38-0.3 fedora 125 k
fedora-release noarch 38-0.6 fedora 11 k
fedora-release-common noarch 38-0.6 fedora 21 k
fedora-release-identity-basic noarch 38-0.6 fedora 11 k
fedora-repos noarch 38-0.3 fedora 10 k
fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k
file-libs ppc64le 5.42-4.fc37 fedora 688 k
filesystem ppc64le 3.18-2.fc37 fedora 1.1 M
findutils ppc64le 1:4.9.0-2.fc37 fedora 538 k
gawk ppc64le 5.1.1-4.fc37 fedora 1.0 M
gdbm-libs ppc64le 1:1.23-2.fc37 fedora 62 k
glib2 ppc64le 2.74.1-2.fc38 fedora 2.9 M
glibc ppc64le 2.36.9000-18.fc38 fedora 2.2 M
glibc-common ppc64le 2.36.9000-18.fc38 fedora 322 k
glibc-minimal-langpack ppc64le 2.36.9000-18.fc38 fedora 30 k
gmp ppc64le 1:6.2.1-3.fc37 fedora 302 k
gnupg2 ppc64le 2.3.8-1.fc38 fedora 2.7 M
gnutls ppc64le 3.7.8-9.fc38 fedora 1.1 M
gpgme ppc64le 1.17.1-3.fc38 fedora 229 k
grep ppc64le 3.8-1.fc38 fedora 303 k
ima-evm-utils ppc64le 1.4-6.fc37 fedora 66 k
json-c ppc64le 0.16-3.fc38 fedora 46 k
keyutils-libs ppc64le 1.6.1-5.fc37 fedora 32 k
krb5-libs ppc64le 1.20.1-3.fc38 fedora 810 k
libacl ppc64le 2.3.1-4.fc38 copr_base 26 k
libarchive ppc64le 3.6.1-3.fc38 fedora 463 k
libassuan ppc64le 2.5.5-5.fc37 fedora 70 k
libattr ppc64le 2.5.1-5.fc38 copr_base 19 k
libb2 ppc64le 0.98.1-7.fc37 fedora 26 k
libblkid ppc64le 2.38.1-3.fc38 fedora 122 k
libbrotli ppc64le 1.0.9-9.fc37 fedora 343 k
libcap ppc64le 2.48-5.fc37 fedora 72 k
libcap-ng ppc64le 0.8.3-4.fc38 fedora 33 k
libcom_err ppc64le 1.46.5-3.fc37 fedora 26 k
libcomps ppc64le 0.1.18-4.fc37 fedora 84 k
libcurl ppc64le 7.87.0-1.fc38 fedora 334 k
libdnf ppc64le 0.68.0-1.fc38 fedora 681 k
libevent ppc64le 2.1.12-7.fc37 fedora 277 k
libffi ppc64le 3.4.4-1.fc38 fedora 38 k
libfsverity ppc64le 1.4-8.fc37 fedora 20 k
libgcc ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 88 k
libgcrypt ppc64le 1.10.1-6.fc38 fedora 591 k
libgomp ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 314 k
libgpg-error ppc64le 1.46-1.fc38 fedora 238 k
libidn2 ppc64le 2.3.4-1.fc38 fedora 163 k
libksba ppc64le 1.6.3-1.fc38 fedora 174 k
libmodulemd ppc64le 2.14.0-4.fc37 fedora 221 k
libmount ppc64le 2.38.1-3.fc38 fedora 154 k
libnghttp2 ppc64le 1.51.0-1.fc38 fedora 84 k
libnsl2 ppc64le 2.0.0-4.fc37 fedora 32 k
libpsl ppc64le 0.21.1-6.fc37 fedora 65 k
librepo ppc64le 1.15.1-1.fc38 fedora 103 k
libreport-filesystem noarch 2.17.6-1.fc38 fedora 14 k
libselinux ppc64le 3.4-6.fc38 fedora 99 k
libsemanage ppc64le 3.4-6.fc38 fedora 131 k
libsepol ppc64le 3.4-4.fc38 fedora 356 k
libsigsegv ppc64le 2.14-3.fc37 fedora 28 k
libsmartcols ppc64le 2.38.1-3.fc38 fedora 70 k
libsolv ppc64le 0.7.22-3.fc37 fedora 467 k
libssh ppc64le 0.10.4-2.fc38 fedora 235 k
libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k
libstdc++ ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 932 k
libtasn1 ppc64le 4.19.0-1.fc38 fedora 80 k
libtirpc ppc64le 1.3.3-0.fc37 fedora 108 k
libunistring ppc64le 1.0-2.fc37 fedora 586 k
libuuid ppc64le 2.38.1-3.fc38 fedora 29 k
libverto ppc64le 0.3.2-4.fc37 fedora 22 k
libxcrypt ppc64le 4.4.33-5.fc38 fedora 132 k
libxml2 ppc64le 2.10.3-2.fc38 fedora 781 k
libyaml ppc64le 0.2.5-8.fc37 fedora 70 k
libzstd ppc64le 1.5.2-3.fc37 fedora 316 k
lua-libs ppc64le 5.4.4-6.fc38 fedora 148 k
lz4-libs ppc64le 1.9.3-5.fc37 fedora 89 k
mpdecimal ppc64le 2.5.1-4.fc37 fedora 117 k
mpfr ppc64le 4.1.1-2.fc38 fedora 608 k
ncurses-base noarch 6.3-5.20221126.fc38 fedora 86 k
ncurses-libs ppc64le 6.3-5.20221126.fc38 fedora 374 k
nettle ppc64le 3.8-2.fc37 fedora 442 k
npth ppc64le 1.6-10.fc38 fedora 24 k
openldap ppc64le 2.6.3-1.fc38 fedora 287 k
openssl-libs ppc64le 1:3.0.5-6.fc38 fedora 2.2 M
p11-kit ppc64le 0.24.1-5.fc38 fedora 374 k
p11-kit-trust ppc64le 0.24.1-5.fc38 fedora 149 k
pcre2 ppc64le 10.40-1.fc37.1 fedora 240 k
pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k
popt ppc64le 1.19-1.fc38 fedora 71 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k
python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M
python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k
python3 ppc64le 3.11.1-1.fc38 fedora 27 k
python3-dateutil noarch 1:2.8.2-4.fc37 fedora 361 k
python3-dbus ppc64le 1.3.2-1.fc38 fedora 162 k
python3-distro noarch 1.8.0-1.fc38 fedora 49 k
python3-dnf noarch 4.14.0-1.fc38 fedora 607 k
python3-dnf-plugins-core noarch 4.3.1-1.fc38 fedora 277 k
python3-gpg ppc64le 1.17.1-3.fc38 fedora 300 k
python3-hawkey ppc64le 0.68.0-1.fc38 fedora 108 k
python3-libcomps ppc64le 0.1.18-4.fc37 fedora 52 k
python3-libdnf ppc64le 0.68.0-1.fc38 fedora 819 k
python3-libs ppc64le 3.11.1-1.fc38 fedora 9.7 M
python3-rpm ppc64le 4.18.0-8.fc38 fedora 101 k
python3-six noarch 1.16.0-8.fc37 fedora 42 k
readline ppc64le 8.2-2.fc38 fedora 228 k
rpm ppc64le 4.18.0-8.fc38 fedora 568 k
rpm-build-libs ppc64le 4.18.0-8.fc38 fedora 103 k
rpm-libs ppc64le 4.18.0-8.fc38 fedora 355 k
rpm-sequoia ppc64le 1.2.0-1.fc38 fedora 1.4 M
rpm-sign-libs ppc64le 4.18.0-8.fc38 fedora 27 k
sed ppc64le 4.8-11.fc37 fedora 313 k
setup noarch 2.14.3-1.fc38 fedora 152 k
shadow-utils ppc64le 2:4.13-3.fc38 fedora 1.3 M
sqlite-libs ppc64le 3.40.0-1.fc38 fedora 776 k
systemd-libs ppc64le 252.4-598.fc38 fedora 666 k
tpm2-tss ppc64le 4.0.0-0.1.rc2.fc38 fedora 631 k
tzdata noarch 2022g-1.fc38 fedora 716 k
xz-libs ppc64le 5.2.9-1.fc38 fedora 104 k
zchunk-libs ppc64le 1.2.3-1.fc38 fedora 55 k
zlib ppc64le 1.2.13-1.fc38 fedora 100 k
Transaction Summary
==========================================================================================================================
Install 137 Packages
Total download size: 60 M
Installed size: 284 M
Downloading Packages:
(1/137): libacl-2.3.1-4.fc38.ppc64le.rpm 149 kB/s | 26 kB 00:00
(2/137): audit-libs-3.0.9-1.fc38.ppc64le.rpm 643 kB/s | 131 kB 00:00
(3/137): libattr-2.5.1-5.fc38.ppc64le.rpm 662 kB/s | 19 kB 00:00
(4/137): bash-5.2.9-3.fc38.ppc64le.rpm 8.0 MB/s | 1.9 MB 00:00
(5/137): libgcc-13.0.0-0.4.fc38.ppc64le.rpm 369 kB/s | 88 kB 00:00
(6/137): libgomp-13.0.0-0.4.fc38.ppc64le.rpm 1.0 MB/s | 314 kB 00:00
(7/137): alternatives-1.21-1.fc38.ppc64le.rpm 510 kB/s | 40 kB 00:00
(8/137): libstdc++-13.0.0-0.4.fc38.ppc64le.rpm 4.2 MB/s | 932 kB 00:00
(9/137): basesystem-11-14.fc37.noarch.rpm 162 kB/s | 7.0 kB 00:00
(10/137): bzip2-libs-1.0.8-12.fc37.ppc64le.rpm 1.1 MB/s | 47 kB 00:00
(11/137): coreutils-common-9.1-8.fc38.ppc64le.r 13 MB/s | 2.0 MB 00:00
(12/137): coreutils-9.1-8.fc38.ppc64le.rpm 7.5 MB/s | 1.4 MB 00:00
(13/137): ca-certificates-2022.2.54-5.fc37.noar 4.2 MB/s | 829 kB 00:00
(14/137): crypto-policies-20221215-1.gita4c31a3 3.8 MB/s | 90 kB 00:00
(15/137): curl-7.87.0-1.fc38.ppc64le.rpm 12 MB/s | 348 kB 00:00
(16/137): dbus-libs-1.14.4-1.fc38.ppc64le.rpm 5.2 MB/s | 176 kB 00:00
(17/137): cyrus-sasl-lib-2.1.28-8.fc38.ppc64le. 17 MB/s | 881 kB 00:00
(18/137): dnf-4.14.0-1.fc38.noarch.rpm 14 MB/s | 480 kB 00:00
(19/137): dnf-data-4.14.0-1.fc38.noarch.rpm 1.9 MB/s | 43 kB 00:00
(20/137): dnf-plugins-core-4.3.1-1.fc38.noarch. 1.5 MB/s | 34 kB 00:00
(21/137): elfutils-default-yama-scope-0.188-3.f 708 kB/s | 15 kB 00:00
(22/137): elfutils-libelf-0.188-3.fc38.ppc64le. 8.0 MB/s | 205 kB 00:00
(23/137): elfutils-libs-0.188-3.fc38.ppc64le.rp 11 MB/s | 291 kB 00:00
(24/137): expat-2.5.0-1.fc38.ppc64le.rpm 4.7 MB/s | 117 kB 00:00
(25/137): fedora-gpg-keys-38-0.3.noarch.rpm 5.1 MB/s | 125 kB 00:00
(26/137): fedora-release-38-0.6.noarch.rpm 490 kB/s | 11 kB 00:00
(27/137): fedora-release-common-38-0.6.noarch.r 965 kB/s | 21 kB 00:00
(28/137): fedora-release-identity-basic-38-0.6. 524 kB/s | 11 kB 00:00
(29/137): fedora-repos-38-0.3.noarch.rpm 464 kB/s | 10 kB 00:00
(30/137): fedora-repos-rawhide-38-0.3.noarch.rp 449 kB/s | 9.7 kB 00:00
(31/137): file-libs-5.42-4.fc37.ppc64le.rpm 21 MB/s | 688 kB 00:00
(32/137): findutils-4.9.0-2.fc37.ppc64le.rpm 15 MB/s | 538 kB 00:00
(33/137): filesystem-3.18-2.fc37.ppc64le.rpm 23 MB/s | 1.1 MB 00:00
(34/137): gawk-5.1.1-4.fc37.ppc64le.rpm 27 MB/s | 1.0 MB 00:00
(35/137): gdbm-libs-1.23-2.fc37.ppc64le.rpm 2.5 MB/s | 62 kB 00:00
(36/137): glibc-common-2.36.9000-18.fc38.ppc64l 8.7 MB/s | 322 kB 00:00
(37/137): glibc-minimal-langpack-2.36.9000-18.f 1.3 MB/s | 30 kB 00:00
(38/137): glibc-2.36.9000-18.fc38.ppc64le.rpm 23 MB/s | 2.2 MB 00:00
(39/137): gmp-6.2.1-3.fc37.ppc64le.rpm 7.8 MB/s | 302 kB 00:00
(40/137): glib2-2.74.1-2.fc38.ppc64le.rpm 22 MB/s | 2.9 MB 00:00
(41/137): gpgme-1.17.1-3.fc38.ppc64le.rpm 7.0 MB/s | 229 kB 00:00
(42/137): gnupg2-2.3.8-1.fc38.ppc64le.rpm 30 MB/s | 2.7 MB 00:00
(43/137): gnutls-3.7.8-9.fc38.ppc64le.rpm 11 MB/s | 1.1 MB 00:00
(44/137): grep-3.8-1.fc38.ppc64le.rpm 6.0 MB/s | 303 kB 00:00
(45/137): ima-evm-utils-1.4-6.fc37.ppc64le.rpm 2.8 MB/s | 66 kB 00:00
(46/137): json-c-0.16-3.fc38.ppc64le.rpm 2.0 MB/s | 46 kB 00:00
(47/137): keyutils-libs-1.6.1-5.fc37.ppc64le.rp 1.4 MB/s | 32 kB 00:00
(48/137): krb5-libs-1.20.1-3.fc38.ppc64le.rpm 23 MB/s | 810 kB 00:00
(49/137): libassuan-2.5.5-5.fc37.ppc64le.rpm 2.7 MB/s | 70 kB 00:00
(50/137): libarchive-3.6.1-3.fc38.ppc64le.rpm 13 MB/s | 463 kB 00:00
(51/137): libb2-0.98.1-7.fc37.ppc64le.rpm 1.1 MB/s | 26 kB 00:00
(52/137): libblkid-2.38.1-3.fc38.ppc64le.rpm 5.0 MB/s | 122 kB 00:00
(53/137): libbrotli-1.0.9-9.fc37.ppc64le.rpm 12 MB/s | 343 kB 00:00
(54/137): libcap-2.48-5.fc37.ppc64le.rpm 3.0 MB/s | 72 kB 00:00
(55/137): libcap-ng-0.8.3-4.fc38.ppc64le.rpm 1.4 MB/s | 33 kB 00:00
(56/137): libcom_err-1.46.5-3.fc37.ppc64le.rpm 1.1 MB/s | 26 kB 00:00
(57/137): libcomps-0.1.18-4.fc37.ppc64le.rpm 3.5 MB/s | 84 kB 00:00
(58/137): libcurl-7.87.0-1.fc38.ppc64le.rpm 12 MB/s | 334 kB 00:00
(59/137): libdnf-0.68.0-1.fc38.ppc64le.rpm 20 MB/s | 681 kB 00:00
(60/137): libevent-2.1.12-7.fc37.ppc64le.rpm 10 MB/s | 277 kB 00:00
(61/137): libffi-3.4.4-1.fc38.ppc64le.rpm 1.6 MB/s | 38 kB 00:00
(62/137): libfsverity-1.4-8.fc37.ppc64le.rpm 892 kB/s | 20 kB 00:00
(63/137): libgpg-error-1.46-1.fc38.ppc64le.rpm 8.4 MB/s | 238 kB 00:00
(64/137): libgcrypt-1.10.1-6.fc38.ppc64le.rpm 17 MB/s | 591 kB 00:00
(65/137): libidn2-2.3.4-1.fc38.ppc64le.rpm 6.5 MB/s | 163 kB 00:00
(66/137): libksba-1.6.3-1.fc38.ppc64le.rpm 6.9 MB/s | 174 kB 00:00
(67/137): libmodulemd-2.14.0-4.fc37.ppc64le.rpm 8.6 MB/s | 221 kB 00:00
(68/137): libmount-2.38.1-3.fc38.ppc64le.rpm 6.2 MB/s | 154 kB 00:00
(69/137): libnghttp2-1.51.0-1.fc38.ppc64le.rpm 3.5 MB/s | 84 kB 00:00
(70/137): libnsl2-2.0.0-4.fc37.ppc64le.rpm 1.4 MB/s | 32 kB 00:00
(71/137): libpsl-0.21.1-6.fc37.ppc64le.rpm 2.8 MB/s | 65 kB 00:00
(72/137): librepo-1.15.1-1.fc38.ppc64le.rpm 4.2 MB/s | 103 kB 00:00
(73/137): libreport-filesystem-2.17.6-1.fc38.no 628 kB/s | 14 kB 00:00
(74/137): libselinux-3.4-6.fc38.ppc64le.rpm 4.1 MB/s | 99 kB 00:00
(75/137): libsemanage-3.4-6.fc38.ppc64le.rpm 5.3 MB/s | 131 kB 00:00
(76/137): libsepol-3.4-4.fc38.ppc64le.rpm 13 MB/s | 356 kB 00:00
(77/137): libsigsegv-2.14-3.fc37.ppc64le.rpm 1.2 MB/s | 28 kB 00:00
(78/137): libsmartcols-2.38.1-3.fc38.ppc64le.rp 3.0 MB/s | 70 kB 00:00
(79/137): libsolv-0.7.22-3.fc37.ppc64le.rpm 16 MB/s | 467 kB 00:00
(80/137): libssh-0.10.4-2.fc38.ppc64le.rpm 7.7 MB/s | 235 kB 00:00
(81/137): libssh-config-0.10.4-2.fc38.noarch.rp 402 kB/s | 8.8 kB 00:00
(82/137): libtasn1-4.19.0-1.fc38.ppc64le.rpm 3.3 MB/s | 80 kB 00:00
(83/137): libtirpc-1.3.3-0.fc37.ppc64le.rpm 4.5 MB/s | 108 kB 00:00
(84/137): libunistring-1.0-2.fc37.ppc64le.rpm 19 MB/s | 586 kB 00:00
(85/137): libuuid-2.38.1-3.fc38.ppc64le.rpm 1.3 MB/s | 29 kB 00:00
(86/137): libverto-0.3.2-4.fc37.ppc64le.rpm 1.0 MB/s | 22 kB 00:00
(87/137): libxcrypt-4.4.33-5.fc38.ppc64le.rpm 5.3 MB/s | 132 kB 00:00
(88/137): libyaml-0.2.5-8.fc37.ppc64le.rpm 2.8 MB/s | 70 kB 00:00
(89/137): libxml2-2.10.3-2.fc38.ppc64le.rpm 20 MB/s | 781 kB 00:00
(90/137): libzstd-1.5.2-3.fc37.ppc64le.rpm 12 MB/s | 316 kB 00:00
(91/137): lua-libs-5.4.4-6.fc38.ppc64le.rpm 6.0 MB/s | 148 kB 00:00
(92/137): lz4-libs-1.9.3-5.fc37.ppc64le.rpm 3.7 MB/s | 89 kB 00:00
(93/137): mpdecimal-2.5.1-4.fc37.ppc64le.rpm 4.8 MB/s | 117 kB 00:00
(94/137): mpfr-4.1.1-2.fc38.ppc64le.rpm 18 MB/s | 608 kB 00:00
(95/137): ncurses-base-6.3-5.20221126.fc38.noar 3.2 MB/s | 86 kB 00:00
(96/137): ncurses-libs-6.3-5.20221126.fc38.ppc6 13 MB/s | 374 kB 00:00
(97/137): npth-1.6-10.fc38.ppc64le.rpm 1.0 MB/s | 24 kB 00:00
(98/137): nettle-3.8-2.fc37.ppc64le.rpm 15 MB/s | 442 kB 00:00
(99/137): openldap-2.6.3-1.fc38.ppc64le.rpm 11 MB/s | 287 kB 00:00
(100/137): p11-kit-0.24.1-5.fc38.ppc64le.rpm 11 MB/s | 374 kB 00:00
(101/137): p11-kit-trust-0.24.1-5.fc38.ppc64le. 4.5 MB/s | 149 kB 00:00
(102/137): openssl-libs-3.0.5-6.fc38.ppc64le.rp 35 MB/s | 2.2 MB 00:00
(103/137): pcre2-10.40-1.fc37.1.ppc64le.rpm 8.1 MB/s | 240 kB 00:00
(104/137): pcre2-syntax-10.40-1.fc37.1.noarch.r 5.8 MB/s | 142 kB 00:00
(105/137): popt-1.19-1.fc38.ppc64le.rpm 3.0 MB/s | 71 kB 00:00
(106/137): publicsuffix-list-dafsa-20221208-1.f 2.5 MB/s | 59 kB 00:00
(107/137): python-pip-wheel-22.3.1-1.fc38.noarc 32 MB/s | 1.4 MB 00:00
(108/137): python3-3.11.1-1.fc38.ppc64le.rpm 1.0 MB/s | 27 kB 00:00
(109/137): python-setuptools-wheel-65.5.1-1.fc3 18 MB/s | 715 kB 00:00
(110/137): python3-dateutil-2.8.2-4.fc37.noarch 13 MB/s | 361 kB 00:00
(111/137): python3-dbus-1.3.2-1.fc38.ppc64le.rp 5.4 MB/s | 162 kB 00:00
(112/137): python3-distro-1.8.0-1.fc38.noarch.r 2.2 MB/s | 49 kB 00:00
(113/137): python3-dnf-4.14.0-1.fc38.noarch.rpm 19 MB/s | 607 kB 00:00
(114/137): python3-dnf-plugins-core-4.3.1-1.fc3 8.2 MB/s | 277 kB 00:00
(115/137): python3-gpg-1.17.1-3.fc38.ppc64le.rp 8.6 MB/s | 300 kB 00:00
(116/137): python3-hawkey-0.68.0-1.fc38.ppc64le 4.4 MB/s | 108 kB 00:00
(117/137): python3-libcomps-0.1.18-4.fc37.ppc64 2.2 MB/s | 52 kB 00:00
(118/137): python3-libdnf-0.68.0-1.fc38.ppc64le 24 MB/s | 819 kB 00:00
(119/137): python3-rpm-4.18.0-8.fc38.ppc64le.rp 3.8 MB/s | 101 kB 00:00
(120/137): python3-six-1.16.0-8.fc37.noarch.rpm 1.3 MB/s | 42 kB 00:00
(121/137): readline-8.2-2.fc38.ppc64le.rpm 7.6 MB/s | 228 kB 00:00
(122/137): rpm-4.18.0-8.fc38.ppc64le.rpm 16 MB/s | 568 kB 00:00
(123/137): rpm-build-libs-4.18.0-8.fc38.ppc64le 3.8 MB/s | 103 kB 00:00
(124/137): rpm-libs-4.18.0-8.fc38.ppc64le.rpm 12 MB/s | 355 kB 00:00
(125/137): rpm-sign-libs-4.18.0-8.fc38.ppc64le. 1.0 MB/s | 27 kB 00:00
(126/137): sed-4.8-11.fc37.ppc64le.rpm 11 MB/s | 313 kB 00:00
(127/137): python3-libs-3.11.1-1.fc38.ppc64le.r 43 MB/s | 9.7 MB 00:00
(128/137): setup-2.14.3-1.fc38.noarch.rpm 2.4 MB/s | 152 kB 00:00
(129/137): rpm-sequoia-1.2.0-1.fc38.ppc64le.rpm 9.3 MB/s | 1.4 MB 00:00
(130/137): sqlite-libs-3.40.0-1.fc38.ppc64le.rp 20 MB/s | 776 kB 00:00
(131/137): shadow-utils-4.13-3.fc38.ppc64le.rpm 24 MB/s | 1.3 MB 00:00
(132/137): systemd-libs-252.4-598.fc38.ppc64le. 13 MB/s | 666 kB 00:00
(133/137): tpm2-tss-4.0.0-0.1.rc2.fc38.ppc64le. 20 MB/s | 631 kB 00:00
(134/137): tzdata-2022g-1.fc38.noarch.rpm 22 MB/s | 716 kB 00:00
(135/137): xz-libs-5.2.9-1.fc38.ppc64le.rpm 3.8 MB/s | 104 kB 00:00
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(137/137): zlib-1.2.13-1.fc38.ppc64le.rpm 3.9 MB/s | 100 kB 00:00
--------------------------------------------------------------------------------
Total 26 MB/s | 60 MB 00:02
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xEB10B464:
Userid : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
fedora 1.6 MB/s | 1.6 kB 00:00
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x5323552A:
Userid : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.ppc64le 1/1
Preparing : 1/1
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warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew
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Installing : glibc-minimal-langpack-2.36.9000-18.fc38.ppc64le 24/137
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useradd: Warning: missing or non-executable shell '/usr/sbin/nologin'
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Verifying : fedora-repos-rawhide-38-0.3.noarch 30/137
Verifying : file-libs-5.42-4.fc37.ppc64le 31/137
Verifying : filesystem-3.18-2.fc37.ppc64le 32/137
Verifying : findutils-1:4.9.0-2.fc37.ppc64le 33/137
Verifying : gawk-5.1.1-4.fc37.ppc64le 34/137
Verifying : gdbm-libs-1:1.23-2.fc37.ppc64le 35/137
Verifying : glib2-2.74.1-2.fc38.ppc64le 36/137
Verifying : glibc-2.36.9000-18.fc38.ppc64le 37/137
Verifying : glibc-common-2.36.9000-18.fc38.ppc64le 38/137
Verifying : glibc-minimal-langpack-2.36.9000-18.fc38.ppc64le 39/137
Verifying : gmp-1:6.2.1-3.fc37.ppc64le 40/137
Verifying : gnupg2-2.3.8-1.fc38.ppc64le 41/137
Verifying : gnutls-3.7.8-9.fc38.ppc64le 42/137
Verifying : gpgme-1.17.1-3.fc38.ppc64le 43/137
Verifying : grep-3.8-1.fc38.ppc64le 44/137
Verifying : ima-evm-utils-1.4-6.fc37.ppc64le 45/137
Verifying : json-c-0.16-3.fc38.ppc64le 46/137
Verifying : keyutils-libs-1.6.1-5.fc37.ppc64le 47/137
Verifying : krb5-libs-1.20.1-3.fc38.ppc64le 48/137
Verifying : libarchive-3.6.1-3.fc38.ppc64le 49/137
Verifying : libassuan-2.5.5-5.fc37.ppc64le 50/137
Verifying : libb2-0.98.1-7.fc37.ppc64le 51/137
Verifying : libblkid-2.38.1-3.fc38.ppc64le 52/137
Verifying : libbrotli-1.0.9-9.fc37.ppc64le 53/137
Verifying : libcap-2.48-5.fc37.ppc64le 54/137
Verifying : libcap-ng-0.8.3-4.fc38.ppc64le 55/137
Verifying : libcom_err-1.46.5-3.fc37.ppc64le 56/137
Verifying : libcomps-0.1.18-4.fc37.ppc64le 57/137
Verifying : libcurl-7.87.0-1.fc38.ppc64le 58/137
Verifying : libdnf-0.68.0-1.fc38.ppc64le 59/137
Verifying : libevent-2.1.12-7.fc37.ppc64le 60/137
Verifying : libffi-3.4.4-1.fc38.ppc64le 61/137
Verifying : libfsverity-1.4-8.fc37.ppc64le 62/137
Verifying : libgcrypt-1.10.1-6.fc38.ppc64le 63/137
Verifying : libgpg-error-1.46-1.fc38.ppc64le 64/137
Verifying : libidn2-2.3.4-1.fc38.ppc64le 65/137
Verifying : libksba-1.6.3-1.fc38.ppc64le 66/137
Verifying : libmodulemd-2.14.0-4.fc37.ppc64le 67/137
Verifying : libmount-2.38.1-3.fc38.ppc64le 68/137
Verifying : libnghttp2-1.51.0-1.fc38.ppc64le 69/137
Verifying : libnsl2-2.0.0-4.fc37.ppc64le 70/137
Verifying : libpsl-0.21.1-6.fc37.ppc64le 71/137
Verifying : librepo-1.15.1-1.fc38.ppc64le 72/137
Verifying : libreport-filesystem-2.17.6-1.fc38.noarch 73/137
Verifying : libselinux-3.4-6.fc38.ppc64le 74/137
Verifying : libsemanage-3.4-6.fc38.ppc64le 75/137
Verifying : libsepol-3.4-4.fc38.ppc64le 76/137
Verifying : libsigsegv-2.14-3.fc37.ppc64le 77/137
Verifying : libsmartcols-2.38.1-3.fc38.ppc64le 78/137
Verifying : libsolv-0.7.22-3.fc37.ppc64le 79/137
Verifying : libssh-0.10.4-2.fc38.ppc64le 80/137
Verifying : libssh-config-0.10.4-2.fc38.noarch 81/137
Verifying : libtasn1-4.19.0-1.fc38.ppc64le 82/137
Verifying : libtirpc-1.3.3-0.fc37.ppc64le 83/137
Verifying : libunistring-1.0-2.fc37.ppc64le 84/137
Verifying : libuuid-2.38.1-3.fc38.ppc64le 85/137
Verifying : libverto-0.3.2-4.fc37.ppc64le 86/137
Verifying : libxcrypt-4.4.33-5.fc38.ppc64le 87/137
Verifying : libxml2-2.10.3-2.fc38.ppc64le 88/137
Verifying : libyaml-0.2.5-8.fc37.ppc64le 89/137
Verifying : libzstd-1.5.2-3.fc37.ppc64le 90/137
Verifying : lua-libs-5.4.4-6.fc38.ppc64le 91/137
Verifying : lz4-libs-1.9.3-5.fc37.ppc64le 92/137
Verifying : mpdecimal-2.5.1-4.fc37.ppc64le 93/137
Verifying : mpfr-4.1.1-2.fc38.ppc64le 94/137
Verifying : ncurses-base-6.3-5.20221126.fc38.noarch 95/137
Verifying : ncurses-libs-6.3-5.20221126.fc38.ppc64le 96/137
Verifying : nettle-3.8-2.fc37.ppc64le 97/137
Verifying : npth-1.6-10.fc38.ppc64le 98/137
Verifying : openldap-2.6.3-1.fc38.ppc64le 99/137
Verifying : openssl-libs-1:3.0.5-6.fc38.ppc64le 100/137
Verifying : p11-kit-0.24.1-5.fc38.ppc64le 101/137
Verifying : p11-kit-trust-0.24.1-5.fc38.ppc64le 102/137
Verifying : pcre2-10.40-1.fc37.1.ppc64le 103/137
Verifying : pcre2-syntax-10.40-1.fc37.1.noarch 104/137
Verifying : popt-1.19-1.fc38.ppc64le 105/137
Verifying : publicsuffix-list-dafsa-20221208-1.fc38.noarch 106/137
Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 107/137
Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 108/137
Verifying : python3-3.11.1-1.fc38.ppc64le 109/137
Verifying : python3-dateutil-1:2.8.2-4.fc37.noarch 110/137
Verifying : python3-dbus-1.3.2-1.fc38.ppc64le 111/137
Verifying : python3-distro-1.8.0-1.fc38.noarch 112/137
Verifying : python3-dnf-4.14.0-1.fc38.noarch 113/137
Verifying : python3-dnf-plugins-core-4.3.1-1.fc38.noarch 114/137
Verifying : python3-gpg-1.17.1-3.fc38.ppc64le 115/137
Verifying : python3-hawkey-0.68.0-1.fc38.ppc64le 116/137
Verifying : python3-libcomps-0.1.18-4.fc37.ppc64le 117/137
Verifying : python3-libdnf-0.68.0-1.fc38.ppc64le 118/137
Verifying : python3-libs-3.11.1-1.fc38.ppc64le 119/137
Verifying : python3-rpm-4.18.0-8.fc38.ppc64le 120/137
Verifying : python3-six-1.16.0-8.fc37.noarch 121/137
Verifying : readline-8.2-2.fc38.ppc64le 122/137
Verifying : rpm-4.18.0-8.fc38.ppc64le 123/137
Verifying : rpm-build-libs-4.18.0-8.fc38.ppc64le 124/137
Verifying : rpm-libs-4.18.0-8.fc38.ppc64le 125/137
Verifying : rpm-sequoia-1.2.0-1.fc38.ppc64le 126/137
Verifying : rpm-sign-libs-4.18.0-8.fc38.ppc64le 127/137
Verifying : sed-4.8-11.fc37.ppc64le 128/137
Verifying : setup-2.14.3-1.fc38.noarch 129/137
Verifying : shadow-utils-2:4.13-3.fc38.ppc64le 130/137
Verifying : sqlite-libs-3.40.0-1.fc38.ppc64le 131/137
Verifying : systemd-libs-252.4-598.fc38.ppc64le 132/137
Verifying : tpm2-tss-4.0.0-0.1.rc2.fc38.ppc64le 133/137
Verifying : tzdata-2022g-1.fc38.noarch 134/137
Verifying : xz-libs-5.2.9-1.fc38.ppc64le 135/137
Verifying : zchunk-libs-1.2.3-1.fc38.ppc64le 136/137
Verifying : zlib-1.2.13-1.fc38.ppc64le 137/137
Installed products updated.
Installed:
alternatives-1.21-1.fc38.ppc64le
audit-libs-3.0.9-1.fc38.ppc64le
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.ppc64le
bzip2-libs-1.0.8-12.fc37.ppc64le
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.ppc64le
coreutils-common-9.1-8.fc38.ppc64le
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.ppc64le
cyrus-sasl-lib-2.1.28-8.fc38.ppc64le
dbus-libs-1:1.14.4-1.fc38.ppc64le
dnf-4.14.0-1.fc38.noarch
dnf-data-4.14.0-1.fc38.noarch
dnf-plugins-core-4.3.1-1.fc38.noarch
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.ppc64le
elfutils-libs-0.188-3.fc38.ppc64le
expat-2.5.0-1.fc38.ppc64le
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-libs-5.42-4.fc37.ppc64le
filesystem-3.18-2.fc37.ppc64le
findutils-1:4.9.0-2.fc37.ppc64le
gawk-5.1.1-4.fc37.ppc64le
gdbm-libs-1:1.23-2.fc37.ppc64le
glib2-2.74.1-2.fc38.ppc64le
glibc-2.36.9000-18.fc38.ppc64le
glibc-common-2.36.9000-18.fc38.ppc64le
glibc-minimal-langpack-2.36.9000-18.fc38.ppc64le
gmp-1:6.2.1-3.fc37.ppc64le
gnupg2-2.3.8-1.fc38.ppc64le
gnutls-3.7.8-9.fc38.ppc64le
gpgme-1.17.1-3.fc38.ppc64le
grep-3.8-1.fc38.ppc64le
ima-evm-utils-1.4-6.fc37.ppc64le
json-c-0.16-3.fc38.ppc64le
keyutils-libs-1.6.1-5.fc37.ppc64le
krb5-libs-1.20.1-3.fc38.ppc64le
libacl-2.3.1-4.fc38.ppc64le
libarchive-3.6.1-3.fc38.ppc64le
libassuan-2.5.5-5.fc37.ppc64le
libattr-2.5.1-5.fc38.ppc64le
libb2-0.98.1-7.fc37.ppc64le
libblkid-2.38.1-3.fc38.ppc64le
libbrotli-1.0.9-9.fc37.ppc64le
libcap-2.48-5.fc37.ppc64le
libcap-ng-0.8.3-4.fc38.ppc64le
libcom_err-1.46.5-3.fc37.ppc64le
libcomps-0.1.18-4.fc37.ppc64le
libcurl-7.87.0-1.fc38.ppc64le
libdnf-0.68.0-1.fc38.ppc64le
libevent-2.1.12-7.fc37.ppc64le
libffi-3.4.4-1.fc38.ppc64le
libfsverity-1.4-8.fc37.ppc64le
libgcc-13.0.0-0.4.fc38.ppc64le
libgcrypt-1.10.1-6.fc38.ppc64le
libgomp-13.0.0-0.4.fc38.ppc64le
libgpg-error-1.46-1.fc38.ppc64le
libidn2-2.3.4-1.fc38.ppc64le
libksba-1.6.3-1.fc38.ppc64le
libmodulemd-2.14.0-4.fc37.ppc64le
libmount-2.38.1-3.fc38.ppc64le
libnghttp2-1.51.0-1.fc38.ppc64le
libnsl2-2.0.0-4.fc37.ppc64le
libpsl-0.21.1-6.fc37.ppc64le
librepo-1.15.1-1.fc38.ppc64le
libreport-filesystem-2.17.6-1.fc38.noarch
libselinux-3.4-6.fc38.ppc64le
libsemanage-3.4-6.fc38.ppc64le
libsepol-3.4-4.fc38.ppc64le
libsigsegv-2.14-3.fc37.ppc64le
libsmartcols-2.38.1-3.fc38.ppc64le
libsolv-0.7.22-3.fc37.ppc64le
libssh-0.10.4-2.fc38.ppc64le
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.ppc64le
libtasn1-4.19.0-1.fc38.ppc64le
libtirpc-1.3.3-0.fc37.ppc64le
libunistring-1.0-2.fc37.ppc64le
libuuid-2.38.1-3.fc38.ppc64le
libverto-0.3.2-4.fc37.ppc64le
libxcrypt-4.4.33-5.fc38.ppc64le
libxml2-2.10.3-2.fc38.ppc64le
libyaml-0.2.5-8.fc37.ppc64le
libzstd-1.5.2-3.fc37.ppc64le
lua-libs-5.4.4-6.fc38.ppc64le
lz4-libs-1.9.3-5.fc37.ppc64le
mpdecimal-2.5.1-4.fc37.ppc64le
mpfr-4.1.1-2.fc38.ppc64le
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.ppc64le
nettle-3.8-2.fc37.ppc64le
npth-1.6-10.fc38.ppc64le
openldap-2.6.3-1.fc38.ppc64le
openssl-libs-1:3.0.5-6.fc38.ppc64le
p11-kit-0.24.1-5.fc38.ppc64le
p11-kit-trust-0.24.1-5.fc38.ppc64le
pcre2-10.40-1.fc37.1.ppc64le
pcre2-syntax-10.40-1.fc37.1.noarch
popt-1.19-1.fc38.ppc64le
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-pip-wheel-22.3.1-1.fc38.noarch
python-setuptools-wheel-65.5.1-1.fc38.noarch
python3-3.11.1-1.fc38.ppc64le
python3-dateutil-1:2.8.2-4.fc37.noarch
python3-dbus-1.3.2-1.fc38.ppc64le
python3-distro-1.8.0-1.fc38.noarch
python3-dnf-4.14.0-1.fc38.noarch
python3-dnf-plugins-core-4.3.1-1.fc38.noarch
python3-gpg-1.17.1-3.fc38.ppc64le
python3-hawkey-0.68.0-1.fc38.ppc64le
python3-libcomps-0.1.18-4.fc37.ppc64le
python3-libdnf-0.68.0-1.fc38.ppc64le
python3-libs-3.11.1-1.fc38.ppc64le
python3-rpm-4.18.0-8.fc38.ppc64le
python3-six-1.16.0-8.fc37.noarch
readline-8.2-2.fc38.ppc64le
rpm-4.18.0-8.fc38.ppc64le
rpm-build-libs-4.18.0-8.fc38.ppc64le
rpm-libs-4.18.0-8.fc38.ppc64le
rpm-sequoia-1.2.0-1.fc38.ppc64le
rpm-sign-libs-4.18.0-8.fc38.ppc64le
sed-4.8-11.fc37.ppc64le
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.ppc64le
sqlite-libs-3.40.0-1.fc38.ppc64le
systemd-libs-252.4-598.fc38.ppc64le
tpm2-tss-4.0.0-0.1.rc2.fc38.ppc64le
tzdata-2022g-1.fc38.noarch
xz-libs-5.2.9-1.fc38.ppc64le
zchunk-libs-1.2.3-1.fc38.ppc64le
zlib-1.2.13-1.fc38.ppc64le
Complete!
Finish(bootstrap): dnf install
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1671784311.816071/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf install
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 11 kB/s | 3.0 kB 00:00
Copr repository 6.3 MB/s | 4.1 MB 00:00
Additional repo https_jakub_fedorapeople_org_fe 8.2 kB/s | 3.0 kB 00:00
fedora 24 kB/s | 6.7 kB 00:00
Dependencies resolved.
==========================================================================================================================
Package Arch Version Repository Size
==========================================================================================================================
Installing group/module packages:
bash ppc64le 5.2.9-3.fc38 copr_base 1.9 M
bzip2 ppc64le 1.0.8-12.fc37 fedora 53 k
coreutils ppc64le 9.1-8.fc38 fedora 1.4 M
cpio ppc64le 2.13-13.fc38 fedora 283 k
diffutils ppc64le 3.8-3.fc37 fedora 389 k
fedora-release-common noarch 38-0.6 fedora 21 k
findutils ppc64le 1:4.9.0-2.fc37 fedora 538 k
gawk ppc64le 5.1.1-4.fc37 fedora 1.0 M
glibc-minimal-langpack ppc64le 2.36.9000-18.fc38 fedora 30 k
grep ppc64le 3.8-1.fc38 fedora 303 k
gzip ppc64le 1.12-2.fc37 fedora 170 k
info ppc64le 7.0.1-1.fc38 fedora 199 k
patch ppc64le 2.7.6-17.fc37 fedora 135 k
redhat-rpm-config noarch 235-1.fc38 fedora 80 k
rpm-build ppc64le 4.18.0-8.fc38 fedora 78 k
sed ppc64le 4.8-11.fc37 fedora 313 k
shadow-utils ppc64le 2:4.13-3.fc38 fedora 1.3 M
tar ppc64le 2:1.34-5.fc38 fedora 914 k
unzip ppc64le 6.0-58.fc38 fedora 188 k
util-linux ppc64le 2.38.1-3.fc38 fedora 2.4 M
which ppc64le 2.21-36.fc38 fedora 42 k
xz ppc64le 5.2.9-1.fc38 fedora 310 k
Installing dependencies:
alternatives ppc64le 1.21-1.fc38 fedora 40 k
ansible-srpm-macros noarch 1-8.1.fc38 fedora 8.6 k
audit-libs ppc64le 3.0.9-1.fc38 copr_base 131 k
authselect ppc64le 1.4.2-1.fc38 copr_base 141 k
authselect-libs ppc64le 1.4.2-1.fc38 copr_base 241 k
basesystem noarch 11-14.fc37 fedora 7.0 k
binutils ppc64le 2.39-6.fc38 copr_base 6.2 M
binutils-gold ppc64le 2.39-6.fc38 copr_base 1.1 M
bzip2-libs ppc64le 1.0.8-12.fc37 fedora 47 k
ca-certificates noarch 2022.2.54-5.fc37 fedora 829 k
coreutils-common ppc64le 9.1-8.fc38 fedora 2.0 M
cracklib ppc64le 2.9.7-30.fc38 fedora 94 k
crypto-policies noarch 20221215-1.gita4c31a3.fc38 fedora 90 k
curl ppc64le 7.87.0-1.fc38 fedora 348 k
cyrus-sasl-lib ppc64le 2.1.28-8.fc38 fedora 881 k
debugedit ppc64le 5.0-5.fc37 fedora 80 k
dwz ppc64le 0.15-1.fc38 fedora 142 k
ed ppc64le 1.18-2.fc37 fedora 81 k
efi-srpm-macros noarch 5-6.fc37 fedora 22 k
elfutils ppc64le 0.188-3.fc38 fedora 559 k
elfutils-debuginfod-client ppc64le 0.188-3.fc38 fedora 41 k
elfutils-default-yama-scope noarch 0.188-3.fc38 fedora 15 k
elfutils-libelf ppc64le 0.188-3.fc38 fedora 205 k
elfutils-libs ppc64le 0.188-3.fc38 fedora 291 k
fedora-gpg-keys noarch 38-0.3 fedora 125 k
fedora-release noarch 38-0.6 fedora 11 k
fedora-release-identity-basic noarch 38-0.6 fedora 11 k
fedora-repos noarch 38-0.3 fedora 10 k
fedora-repos-rawhide noarch 38-0.3 fedora 9.7 k
file ppc64le 5.42-4.fc37 fedora 49 k
file-libs ppc64le 5.42-4.fc37 fedora 688 k
filesystem ppc64le 3.18-2.fc37 fedora 1.1 M
fonts-srpm-macros noarch 1:2.0.5-10.fc38 fedora 26 k
fpc-srpm-macros noarch 1.3-6.fc37 fedora 7.7 k
gdb-minimal ppc64le 12.1-10.fc38 fedora 3.7 M
gdbm-libs ppc64le 1:1.23-2.fc37 fedora 62 k
ghc-srpm-macros noarch 1.5.0-7.fc37 fedora 7.8 k
glibc ppc64le 2.36.9000-18.fc38 fedora 2.2 M
glibc-common ppc64le 2.36.9000-18.fc38 fedora 322 k
glibc-gconv-extra ppc64le 2.36.9000-18.fc38 fedora 1.9 M
gmp ppc64le 1:6.2.1-3.fc37 fedora 302 k
gnat-srpm-macros noarch 4-16.fc37 fedora 8.3 k
go-srpm-macros noarch 3.2.0-1.fc38 fedora 27 k
jansson ppc64le 2.13.1-5.fc37 fedora 50 k
kernel-srpm-macros noarch 1.0-15.fc37 fedora 9.4 k
keyutils-libs ppc64le 1.6.1-5.fc37 fedora 32 k
krb5-libs ppc64le 1.20.1-3.fc38 fedora 810 k
libacl ppc64le 2.3.1-4.fc38 copr_base 26 k
libarchive ppc64le 3.6.1-3.fc38 fedora 463 k
libattr ppc64le 2.5.1-5.fc38 copr_base 19 k
libblkid ppc64le 2.38.1-3.fc38 fedora 122 k
libbrotli ppc64le 1.0.9-9.fc37 fedora 343 k
libcap ppc64le 2.48-5.fc37 fedora 72 k
libcap-ng ppc64le 0.8.3-4.fc38 fedora 33 k
libcom_err ppc64le 1.46.5-3.fc37 fedora 26 k
libcurl ppc64le 7.87.0-1.fc38 fedora 334 k
libdb ppc64le 5.3.28-54.fc38 fedora 841 k
libeconf ppc64le 0.4.0-4.fc37 fedora 30 k
libevent ppc64le 2.1.12-7.fc37 fedora 277 k
libfdisk ppc64le 2.38.1-3.fc38 fedora 176 k
libffi ppc64le 3.4.4-1.fc38 fedora 38 k
libgcc ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 88 k
libgomp ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 314 k
libidn2 ppc64le 2.3.4-1.fc38 fedora 163 k
libmount ppc64le 2.38.1-3.fc38 fedora 154 k
libnghttp2 ppc64le 1.51.0-1.fc38 fedora 84 k
libnsl2 ppc64le 2.0.0-4.fc37 fedora 32 k
libpkgconf ppc64le 1.8.0-3.fc37 fedora 40 k
libpsl ppc64le 0.21.1-6.fc37 fedora 65 k
libpwquality ppc64le 1.4.4-11.fc37 fedora 119 k
librtas ppc64le 2.0.3-1.fc38 fedora 67 k
libselinux ppc64le 3.4-6.fc38 fedora 99 k
libsemanage ppc64le 3.4-6.fc38 fedora 131 k
libsepol ppc64le 3.4-4.fc38 fedora 356 k
libsigsegv ppc64le 2.14-3.fc37 fedora 28 k
libsmartcols ppc64le 2.38.1-3.fc38 fedora 70 k
libssh ppc64le 0.10.4-2.fc38 fedora 235 k
libssh-config noarch 0.10.4-2.fc38 fedora 8.8 k
libstdc++ ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 932 k
libtasn1 ppc64le 4.19.0-1.fc38 fedora 80 k
libtirpc ppc64le 1.3.3-0.fc37 fedora 108 k
libunistring ppc64le 1.0-2.fc37 fedora 586 k
libutempter ppc64le 1.2.1-7.fc37 fedora 27 k
libuuid ppc64le 2.38.1-3.fc38 fedora 29 k
libverto ppc64le 0.3.2-4.fc37 fedora 22 k
libxcrypt ppc64le 4.4.33-5.fc38 fedora 132 k
libxml2 ppc64le 2.10.3-2.fc38 fedora 781 k
libzstd ppc64le 1.5.2-3.fc37 fedora 316 k
lua-libs ppc64le 5.4.4-6.fc38 fedora 148 k
lua-srpm-macros noarch 1-7.fc37 fedora 8.8 k
lz4-libs ppc64le 1.9.3-5.fc37 fedora 89 k
mpfr ppc64le 4.1.1-2.fc38 fedora 608 k
ncurses-base noarch 6.3-5.20221126.fc38 fedora 86 k
ncurses-libs ppc64le 6.3-5.20221126.fc38 fedora 374 k
nettle ppc64le 3.8-2.fc37 fedora 442 k
nim-srpm-macros noarch 3-7.fc37 fedora 8.4 k
ocaml-srpm-macros noarch 7-2.fc37 fedora 13 k
openblas-srpm-macros noarch 2-12.fc37 fedora 7.5 k
openldap ppc64le 2.6.3-1.fc38 fedora 287 k
openssl-libs ppc64le 1:3.0.5-6.fc38 fedora 2.2 M
p11-kit ppc64le 0.24.1-5.fc38 fedora 374 k
p11-kit-trust ppc64le 0.24.1-5.fc38 fedora 149 k
package-notes-srpm-macros noarch 0.5-6.fc38 fedora 11 k
pam ppc64le 1.5.2-15.fc38 fedora 605 k
pam-libs ppc64le 1.5.2-15.fc38 fedora 63 k
pcre2 ppc64le 10.40-1.fc37.1 fedora 240 k
pcre2-syntax noarch 10.40-1.fc37.1 fedora 142 k
perl-srpm-macros noarch 1-47.fc38 fedora 8.2 k
pkgconf ppc64le 1.8.0-3.fc37 fedora 43 k
pkgconf-m4 noarch 1.8.0-3.fc37 fedora 14 k
pkgconf-pkg-config ppc64le 1.8.0-3.fc37 fedora 10 k
popt ppc64le 1.19-1.fc38 fedora 71 k
publicsuffix-list-dafsa noarch 20221208-1.fc38 fedora 59 k
python-srpm-macros noarch 3.11-6.fc38 fedora 25 k
qt5-srpm-macros noarch 5.15.7-1.fc38 fedora 7.9 k
readline ppc64le 8.2-2.fc38 fedora 228 k
rpm ppc64le 4.18.0-8.fc38 fedora 568 k
rpm-build-libs ppc64le 4.18.0-8.fc38 fedora 103 k
rpm-libs ppc64le 4.18.0-8.fc38 fedora 355 k
rpm-sequoia ppc64le 1.2.0-1.fc38 fedora 1.4 M
rpmautospec-rpm-macros noarch 0.3.1-1.fc38 fedora 8.8 k
rust-srpm-macros noarch 23-1.fc38 fedora 9.4 k
setup noarch 2.14.3-1.fc38 fedora 152 k
sqlite-libs ppc64le 3.40.0-1.fc38 fedora 776 k
systemd-libs ppc64le 252.4-598.fc38 fedora 666 k
tzdata noarch 2022g-1.fc38 fedora 716 k
util-linux-core ppc64le 2.38.1-3.fc38 fedora 515 k
xxhash-libs ppc64le 0.8.1-3.fc37 fedora 38 k
xz-libs ppc64le 5.2.9-1.fc38 fedora 104 k
zip ppc64le 3.0-35.fc38 fedora 267 k
zlib ppc64le 1.2.13-1.fc38 fedora 100 k
zstd ppc64le 1.5.2-3.fc37 fedora 466 k
Installing Groups:
Buildsystem building group
Transaction Summary
==========================================================================================================================
Install 154 Packages
Total size: 57 M
Installed size: 328 M
Downloading Packages:
[SKIPPED] audit-libs-3.0.9-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] authselect-1.4.2-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] authselect-libs-1.4.2-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] bash-5.2.9-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] binutils-2.39-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] binutils-gold-2.39-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libacl-2.3.1-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libattr-2.5.1-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libgcc-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libgomp-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libstdc++-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] alternatives-1.21-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] ansible-srpm-macros-1-8.1.fc38.noarch.rpm: Already downloaded
[SKIPPED] basesystem-11-14.fc37.noarch.rpm: Already downloaded
[SKIPPED] bzip2-1.0.8-12.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] bzip2-libs-1.0.8-12.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] ca-certificates-2022.2.54-5.fc37.noarch.rpm: Already downloaded
[SKIPPED] coreutils-9.1-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] coreutils-common-9.1-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] cpio-2.13-13.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] cracklib-2.9.7-30.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] crypto-policies-20221215-1.gita4c31a3.fc38.noarch.rpm: Already downloaded
[SKIPPED] curl-7.87.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] cyrus-sasl-lib-2.1.28-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] debugedit-5.0-5.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] diffutils-3.8-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] dwz-0.15-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] ed-1.18-2.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] efi-srpm-macros-5-6.fc37.noarch.rpm: Already downloaded
[SKIPPED] elfutils-0.188-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-debuginfod-client-0.188-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-default-yama-scope-0.188-3.fc38.noarch.rpm: Already downloaded
[SKIPPED] elfutils-libelf-0.188-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] elfutils-libs-0.188-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] fedora-gpg-keys-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-common-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-release-identity-basic-38-0.6.noarch.rpm: Already downloaded
[SKIPPED] fedora-repos-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] fedora-repos-rawhide-38-0.3.noarch.rpm: Already downloaded
[SKIPPED] file-5.42-4.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] file-libs-5.42-4.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] filesystem-3.18-2.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] findutils-4.9.0-2.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] fonts-srpm-macros-2.0.5-10.fc38.noarch.rpm: Already downloaded
[SKIPPED] fpc-srpm-macros-1.3-6.fc37.noarch.rpm: Already downloaded
[SKIPPED] gawk-5.1.1-4.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] gdb-minimal-12.1-10.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gdbm-libs-1.23-2.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] ghc-srpm-macros-1.5.0-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] glibc-2.36.9000-18.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-common-2.36.9000-18.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-gconv-extra-2.36.9000-18.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-minimal-langpack-2.36.9000-18.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gmp-6.2.1-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] gnat-srpm-macros-4-16.fc37.noarch.rpm: Already downloaded
[SKIPPED] go-srpm-macros-3.2.0-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] grep-3.8-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gzip-1.12-2.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] info-7.0.1-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] jansson-2.13.1-5.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] kernel-srpm-macros-1.0-15.fc37.noarch.rpm: Already downloaded
[SKIPPED] keyutils-libs-1.6.1-5.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] krb5-libs-1.20.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libarchive-3.6.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libblkid-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libbrotli-1.0.9-9.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libcap-2.48-5.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libcap-ng-0.8.3-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libcom_err-1.46.5-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libcurl-7.87.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libdb-5.3.28-54.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libeconf-0.4.0-4.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libevent-2.1.12-7.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libfdisk-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libffi-3.4.4-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libidn2-2.3.4-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libmount-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libnghttp2-1.51.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libnsl2-2.0.0-4.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libpkgconf-1.8.0-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libpsl-0.21.1-6.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libpwquality-1.4.4-11.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] librtas-2.0.3-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libselinux-3.4-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libsemanage-3.4-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libsepol-3.4-4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libsigsegv-2.14-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libsmartcols-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libssh-0.10.4-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libssh-config-0.10.4-2.fc38.noarch.rpm: Already downloaded
[SKIPPED] libtasn1-4.19.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libtirpc-1.3.3-0.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libunistring-1.0-2.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libutempter-1.2.1-7.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libuuid-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libverto-0.3.2-4.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libxcrypt-4.4.33-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libxml2-2.10.3-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libzstd-1.5.2-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] lua-libs-5.4.4-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] lua-srpm-macros-1-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] lz4-libs-1.9.3-5.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] mpfr-4.1.1-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] ncurses-base-6.3-5.20221126.fc38.noarch.rpm: Already downloaded
[SKIPPED] ncurses-libs-6.3-5.20221126.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] nettle-3.8-2.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] nim-srpm-macros-3-7.fc37.noarch.rpm: Already downloaded
[SKIPPED] ocaml-srpm-macros-7-2.fc37.noarch.rpm: Already downloaded
[SKIPPED] openblas-srpm-macros-2-12.fc37.noarch.rpm: Already downloaded
[SKIPPED] openldap-2.6.3-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] openssl-libs-3.0.5-6.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] p11-kit-0.24.1-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] p11-kit-trust-0.24.1-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] package-notes-srpm-macros-0.5-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] pam-1.5.2-15.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] pam-libs-1.5.2-15.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] patch-2.7.6-17.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] pcre2-10.40-1.fc37.1.ppc64le.rpm: Already downloaded
[SKIPPED] pcre2-syntax-10.40-1.fc37.1.noarch.rpm: Already downloaded
[SKIPPED] perl-srpm-macros-1-47.fc38.noarch.rpm: Already downloaded
[SKIPPED] pkgconf-1.8.0-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] pkgconf-m4-1.8.0-3.fc37.noarch.rpm: Already downloaded
[SKIPPED] pkgconf-pkg-config-1.8.0-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] popt-1.19-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] publicsuffix-list-dafsa-20221208-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-srpm-macros-3.11-6.fc38.noarch.rpm: Already downloaded
[SKIPPED] qt5-srpm-macros-5.15.7-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] readline-8.2-2.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] redhat-rpm-config-235-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] rpm-4.18.0-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpm-build-4.18.0-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpm-build-libs-4.18.0-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpm-libs-4.18.0-8.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpm-sequoia-1.2.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] rpmautospec-rpm-macros-0.3.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] rust-srpm-macros-23-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] sed-4.8-11.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] setup-2.14.3-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] shadow-utils-4.13-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] sqlite-libs-3.40.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] systemd-libs-252.4-598.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] tar-1.34-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] tzdata-2022g-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] unzip-6.0-58.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] util-linux-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] util-linux-core-2.38.1-3.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] which-2.21-36.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] xxhash-libs-0.8.1-3.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] xz-5.2.9-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] xz-libs-5.2.9-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] zip-3.0-35.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] zlib-1.2.13-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] zstd-1.5.2-3.fc37.ppc64le.rpm: Already downloaded
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0xEB10B464:
Userid : "Fedora (38) <fedora-38-primary@fedoraproject.org>"
Fingerprint: 6A51 BBAB BA3D 5467 B617 1221 809A 8D7C EB10 B464
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary
Key imported successfully
fedora 1.6 MB/s | 1.6 kB 00:00
GPG key at file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-38-primary (0xEB10B464) is already installed
fedora 1.6 MB/s | 1.6 kB 00:00
Importing GPG key 0x5323552A:
Userid : "Fedora (37) <fedora-37-primary@fedoraproject.org>"
Fingerprint: ACB5 EE4E 831C 74BB 7C16 8D27 F55A D3FB 5323 552A
From : /usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-37-primary
Key imported successfully
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
Running scriptlet: filesystem-3.18-2.fc37.ppc64le 1/1
Preparing : 1/1
Installing : libgcc-13.0.0-0.4.fc38.ppc64le 1/154
Running scriptlet: libgcc-13.0.0-0.4.fc38.ppc64le 1/154
Installing : crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/154
Running scriptlet: crypto-policies-20221215-1.gita4c31a3.fc38.noarc 2/154
Installing : fedora-release-identity-basic-38-0.6.noarch 3/154
Installing : tzdata-2022g-1.fc38.noarch 4/154
Installing : rust-srpm-macros-23-1.fc38.noarch 5/154
Installing : qt5-srpm-macros-5.15.7-1.fc38.noarch 6/154
Installing : publicsuffix-list-dafsa-20221208-1.fc38.noarch 7/154
Installing : pkgconf-m4-1.8.0-3.fc37.noarch 8/154
Installing : perl-srpm-macros-1-47.fc38.noarch 9/154
Installing : pcre2-syntax-10.40-1.fc37.1.noarch 10/154
Installing : package-notes-srpm-macros-0.5-6.fc38.noarch 11/154
Installing : openblas-srpm-macros-2-12.fc37.noarch 12/154
Installing : ocaml-srpm-macros-7-2.fc37.noarch 13/154
Installing : nim-srpm-macros-3-7.fc37.noarch 14/154
Installing : ncurses-base-6.3-5.20221126.fc38.noarch 15/154
Installing : libssh-config-0.10.4-2.fc38.noarch 16/154
Installing : kernel-srpm-macros-1.0-15.fc37.noarch 17/154
Installing : gnat-srpm-macros-4-16.fc37.noarch 18/154
Installing : ghc-srpm-macros-1.5.0-7.fc37.noarch 19/154
Installing : fpc-srpm-macros-1.3-6.fc37.noarch 20/154
Installing : fedora-gpg-keys-38-0.3.noarch 21/154
Installing : fedora-release-38-0.6.noarch 22/154
Installing : fedora-release-common-38-0.6.noarch 23/154
Installing : fedora-repos-rawhide-38-0.3.noarch 24/154
Installing : fedora-repos-38-0.3.noarch 25/154
Installing : setup-2.14.3-1.fc38.noarch 26/154
warning: /etc/hosts created as /etc/hosts.rpmnew
Running scriptlet: setup-2.14.3-1.fc38.noarch 26/154
Installing : filesystem-3.18-2.fc37.ppc64le 27/154
Installing : basesystem-11-14.fc37.noarch 28/154
Installing : glibc-gconv-extra-2.36.9000-18.fc38.ppc64le 29/154
Running scriptlet: glibc-gconv-extra-2.36.9000-18.fc38.ppc64le 29/154
Installing : ncurses-libs-6.3-5.20221126.fc38.ppc64le 30/154
Running scriptlet: glibc-2.36.9000-18.fc38.ppc64le 31/154
Installing : glibc-2.36.9000-18.fc38.ppc64le 31/154
Running scriptlet: glibc-2.36.9000-18.fc38.ppc64le 31/154
Installing : bash-5.2.9-3.fc38.ppc64le 32/154
Running scriptlet: bash-5.2.9-3.fc38.ppc64le 32/154
Installing : glibc-common-2.36.9000-18.fc38.ppc64le 33/154
Installing : glibc-minimal-langpack-2.36.9000-18.fc38.ppc64le 34/154
Installing : zlib-1.2.13-1.fc38.ppc64le 35/154
Installing : xz-libs-5.2.9-1.fc38.ppc64le 36/154
Installing : bzip2-libs-1.0.8-12.fc37.ppc64le 37/154
Installing : elfutils-libelf-0.188-3.fc38.ppc64le 38/154
Installing : gmp-1:6.2.1-3.fc37.ppc64le 39/154
Installing : libstdc++-13.0.0-0.4.fc38.ppc64le 40/154
Installing : libuuid-2.38.1-3.fc38.ppc64le 41/154
Installing : libzstd-1.5.2-3.fc37.ppc64le 42/154
Installing : popt-1.19-1.fc38.ppc64le 43/154
Installing : libblkid-2.38.1-3.fc38.ppc64le 44/154
Installing : libattr-2.5.1-5.fc38.ppc64le 45/154
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Verifying : rpm-4.18.0-8.fc38.ppc64le 131/154
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Verifying : sed-4.8-11.fc37.ppc64le 138/154
Verifying : setup-2.14.3-1.fc38.noarch 139/154
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Installed:
alternatives-1.21-1.fc38.ppc64le
ansible-srpm-macros-1-8.1.fc38.noarch
audit-libs-3.0.9-1.fc38.ppc64le
authselect-1.4.2-1.fc38.ppc64le
authselect-libs-1.4.2-1.fc38.ppc64le
basesystem-11-14.fc37.noarch
bash-5.2.9-3.fc38.ppc64le
binutils-2.39-6.fc38.ppc64le
binutils-gold-2.39-6.fc38.ppc64le
bzip2-1.0.8-12.fc37.ppc64le
bzip2-libs-1.0.8-12.fc37.ppc64le
ca-certificates-2022.2.54-5.fc37.noarch
coreutils-9.1-8.fc38.ppc64le
coreutils-common-9.1-8.fc38.ppc64le
cpio-2.13-13.fc38.ppc64le
cracklib-2.9.7-30.fc38.ppc64le
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
curl-7.87.0-1.fc38.ppc64le
cyrus-sasl-lib-2.1.28-8.fc38.ppc64le
debugedit-5.0-5.fc37.ppc64le
diffutils-3.8-3.fc37.ppc64le
dwz-0.15-1.fc38.ppc64le
ed-1.18-2.fc37.ppc64le
efi-srpm-macros-5-6.fc37.noarch
elfutils-0.188-3.fc38.ppc64le
elfutils-debuginfod-client-0.188-3.fc38.ppc64le
elfutils-default-yama-scope-0.188-3.fc38.noarch
elfutils-libelf-0.188-3.fc38.ppc64le
elfutils-libs-0.188-3.fc38.ppc64le
fedora-gpg-keys-38-0.3.noarch
fedora-release-38-0.6.noarch
fedora-release-common-38-0.6.noarch
fedora-release-identity-basic-38-0.6.noarch
fedora-repos-38-0.3.noarch
fedora-repos-rawhide-38-0.3.noarch
file-5.42-4.fc37.ppc64le
file-libs-5.42-4.fc37.ppc64le
filesystem-3.18-2.fc37.ppc64le
findutils-1:4.9.0-2.fc37.ppc64le
fonts-srpm-macros-1:2.0.5-10.fc38.noarch
fpc-srpm-macros-1.3-6.fc37.noarch
gawk-5.1.1-4.fc37.ppc64le
gdb-minimal-12.1-10.fc38.ppc64le
gdbm-libs-1:1.23-2.fc37.ppc64le
ghc-srpm-macros-1.5.0-7.fc37.noarch
glibc-2.36.9000-18.fc38.ppc64le
glibc-common-2.36.9000-18.fc38.ppc64le
glibc-gconv-extra-2.36.9000-18.fc38.ppc64le
glibc-minimal-langpack-2.36.9000-18.fc38.ppc64le
gmp-1:6.2.1-3.fc37.ppc64le
gnat-srpm-macros-4-16.fc37.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
grep-3.8-1.fc38.ppc64le
gzip-1.12-2.fc37.ppc64le
info-7.0.1-1.fc38.ppc64le
jansson-2.13.1-5.fc37.ppc64le
kernel-srpm-macros-1.0-15.fc37.noarch
keyutils-libs-1.6.1-5.fc37.ppc64le
krb5-libs-1.20.1-3.fc38.ppc64le
libacl-2.3.1-4.fc38.ppc64le
libarchive-3.6.1-3.fc38.ppc64le
libattr-2.5.1-5.fc38.ppc64le
libblkid-2.38.1-3.fc38.ppc64le
libbrotli-1.0.9-9.fc37.ppc64le
libcap-2.48-5.fc37.ppc64le
libcap-ng-0.8.3-4.fc38.ppc64le
libcom_err-1.46.5-3.fc37.ppc64le
libcurl-7.87.0-1.fc38.ppc64le
libdb-5.3.28-54.fc38.ppc64le
libeconf-0.4.0-4.fc37.ppc64le
libevent-2.1.12-7.fc37.ppc64le
libfdisk-2.38.1-3.fc38.ppc64le
libffi-3.4.4-1.fc38.ppc64le
libgcc-13.0.0-0.4.fc38.ppc64le
libgomp-13.0.0-0.4.fc38.ppc64le
libidn2-2.3.4-1.fc38.ppc64le
libmount-2.38.1-3.fc38.ppc64le
libnghttp2-1.51.0-1.fc38.ppc64le
libnsl2-2.0.0-4.fc37.ppc64le
libpkgconf-1.8.0-3.fc37.ppc64le
libpsl-0.21.1-6.fc37.ppc64le
libpwquality-1.4.4-11.fc37.ppc64le
librtas-2.0.3-1.fc38.ppc64le
libselinux-3.4-6.fc38.ppc64le
libsemanage-3.4-6.fc38.ppc64le
libsepol-3.4-4.fc38.ppc64le
libsigsegv-2.14-3.fc37.ppc64le
libsmartcols-2.38.1-3.fc38.ppc64le
libssh-0.10.4-2.fc38.ppc64le
libssh-config-0.10.4-2.fc38.noarch
libstdc++-13.0.0-0.4.fc38.ppc64le
libtasn1-4.19.0-1.fc38.ppc64le
libtirpc-1.3.3-0.fc37.ppc64le
libunistring-1.0-2.fc37.ppc64le
libutempter-1.2.1-7.fc37.ppc64le
libuuid-2.38.1-3.fc38.ppc64le
libverto-0.3.2-4.fc37.ppc64le
libxcrypt-4.4.33-5.fc38.ppc64le
libxml2-2.10.3-2.fc38.ppc64le
libzstd-1.5.2-3.fc37.ppc64le
lua-libs-5.4.4-6.fc38.ppc64le
lua-srpm-macros-1-7.fc37.noarch
lz4-libs-1.9.3-5.fc37.ppc64le
mpfr-4.1.1-2.fc38.ppc64le
ncurses-base-6.3-5.20221126.fc38.noarch
ncurses-libs-6.3-5.20221126.fc38.ppc64le
nettle-3.8-2.fc37.ppc64le
nim-srpm-macros-3-7.fc37.noarch
ocaml-srpm-macros-7-2.fc37.noarch
openblas-srpm-macros-2-12.fc37.noarch
openldap-2.6.3-1.fc38.ppc64le
openssl-libs-1:3.0.5-6.fc38.ppc64le
p11-kit-0.24.1-5.fc38.ppc64le
p11-kit-trust-0.24.1-5.fc38.ppc64le
package-notes-srpm-macros-0.5-6.fc38.noarch
pam-1.5.2-15.fc38.ppc64le
pam-libs-1.5.2-15.fc38.ppc64le
patch-2.7.6-17.fc37.ppc64le
pcre2-10.40-1.fc37.1.ppc64le
pcre2-syntax-10.40-1.fc37.1.noarch
perl-srpm-macros-1-47.fc38.noarch
pkgconf-1.8.0-3.fc37.ppc64le
pkgconf-m4-1.8.0-3.fc37.noarch
pkgconf-pkg-config-1.8.0-3.fc37.ppc64le
popt-1.19-1.fc38.ppc64le
publicsuffix-list-dafsa-20221208-1.fc38.noarch
python-srpm-macros-3.11-6.fc38.noarch
qt5-srpm-macros-5.15.7-1.fc38.noarch
readline-8.2-2.fc38.ppc64le
redhat-rpm-config-235-1.fc38.noarch
rpm-4.18.0-8.fc38.ppc64le
rpm-build-4.18.0-8.fc38.ppc64le
rpm-build-libs-4.18.0-8.fc38.ppc64le
rpm-libs-4.18.0-8.fc38.ppc64le
rpm-sequoia-1.2.0-1.fc38.ppc64le
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
rust-srpm-macros-23-1.fc38.noarch
sed-4.8-11.fc37.ppc64le
setup-2.14.3-1.fc38.noarch
shadow-utils-2:4.13-3.fc38.ppc64le
sqlite-libs-3.40.0-1.fc38.ppc64le
systemd-libs-252.4-598.fc38.ppc64le
tar-2:1.34-5.fc38.ppc64le
tzdata-2022g-1.fc38.noarch
unzip-6.0-58.fc38.ppc64le
util-linux-2.38.1-3.fc38.ppc64le
util-linux-core-2.38.1-3.fc38.ppc64le
which-2.21-36.fc38.ppc64le
xxhash-libs-0.8.1-3.fc37.ppc64le
xz-5.2.9-1.fc38.ppc64le
xz-libs-5.2.9-1.fc38.ppc64le
zip-3.0-35.fc38.ppc64le
zlib-1.2.13-1.fc38.ppc64le
zstd-1.5.2-3.fc37.ppc64le
Complete!
Finish: dnf install
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: tar-1.34-5.fc38.ppc64le
glibc-2.36.9000-18.fc38.ppc64le
glibc-gconv-extra-2.36.9000-18.fc38.ppc64le
rpm-libs-4.18.0-8.fc38.ppc64le
gdb-minimal-12.1-10.fc38.ppc64le
libbrotli-1.0.9-9.fc37.ppc64le
debugedit-5.0-5.fc37.ppc64le
redhat-rpm-config-235-1.fc38.noarch
libverto-0.3.2-4.fc37.ppc64le
xz-libs-5.2.9-1.fc38.ppc64le
filesystem-3.18-2.fc37.ppc64le
xz-5.2.9-1.fc38.ppc64le
pcre2-10.40-1.fc37.1.ppc64le
libcurl-7.87.0-1.fc38.ppc64le
file-libs-5.42-4.fc37.ppc64le
rpm-sequoia-1.2.0-1.fc38.ppc64le
util-linux-core-2.38.1-3.fc38.ppc64le
tzdata-2022g-1.fc38.noarch
efi-srpm-macros-5-6.fc37.noarch
go-srpm-macros-3.2.0-1.fc38.noarch
authselect-1.4.2-1.fc38.ppc64le
popt-1.19-1.fc38.ppc64le
elfutils-default-yama-scope-0.188-3.fc38.noarch
crypto-policies-20221215-1.gita4c31a3.fc38.noarch
libevent-2.1.12-7.fc37.ppc64le
python-srpm-macros-3.11-6.fc38.noarch
perl-srpm-macros-1-47.fc38.noarch
findutils-4.9.0-2.fc37.ppc64le
bash-5.2.9-3.fc38.ppc64le
libeconf-0.4.0-4.fc37.ppc64le
ca-certificates-2022.2.54-5.fc37.noarch
libcap-ng-0.8.3-4.fc38.ppc64le
libnghttp2-1.51.0-1.fc38.ppc64le
info-7.0.1-1.fc38.ppc64le
diffutils-3.8-3.fc37.ppc64le
p11-kit-0.24.1-5.fc38.ppc64le
basesystem-11-14.fc37.noarch
publicsuffix-list-dafsa-20221208-1.fc38.noarch
libnsl2-2.0.0-4.fc37.ppc64le
rust-srpm-macros-23-1.fc38.noarch
pkgconf-pkg-config-1.8.0-3.fc37.ppc64le
systemd-libs-252.4-598.fc38.ppc64le
ansible-srpm-macros-1-8.1.fc38.noarch
ocaml-srpm-macros-7-2.fc37.noarch
libxcrypt-4.4.33-5.fc38.ppc64le
libdb-5.3.28-54.fc38.ppc64le
fedora-gpg-keys-38-0.3.noarch
patch-2.7.6-17.fc37.ppc64le
lua-libs-5.4.4-6.fc38.ppc64le
glibc-common-2.36.9000-18.fc38.ppc64le
p11-kit-trust-0.24.1-5.fc38.ppc64le
curl-7.87.0-1.fc38.ppc64le
zlib-1.2.13-1.fc38.ppc64le
libsepol-3.4-4.fc38.ppc64le
libssh-0.10.4-2.fc38.ppc64le
rpm-build-libs-4.18.0-8.fc38.ppc64le
fedora-repos-rawhide-38-0.3.noarch
authselect-libs-1.4.2-1.fc38.ppc64le
libtasn1-4.19.0-1.fc38.ppc64le
elfutils-0.188-3.fc38.ppc64le
openssl-libs-3.0.5-6.fc38.ppc64le
sed-4.8-11.fc37.ppc64le
which-2.21-36.fc38.ppc64le
util-linux-2.38.1-3.fc38.ppc64le
libsemanage-3.4-6.fc38.ppc64le
gdbm-libs-1.23-2.fc37.ppc64le
rpmautospec-rpm-macros-0.3.1-1.fc38.noarch
elfutils-libelf-0.188-3.fc38.ppc64le
keyutils-libs-1.6.1-5.fc37.ppc64le
coreutils-9.1-8.fc38.ppc64le
qt5-srpm-macros-5.15.7-1.fc38.noarch
libattr-2.5.1-5.fc38.ppc64le
grep-3.8-1.fc38.ppc64le
lua-srpm-macros-1-7.fc37.noarch
alternatives-1.21-1.fc38.ppc64le
zstd-1.5.2-3.fc37.ppc64le
setup-2.14.3-1.fc38.noarch
sqlite-libs-3.40.0-1.fc38.ppc64le
cracklib-2.9.7-30.fc38.ppc64le
gpg-pubkey-5323552a-6112bcdc
libblkid-2.38.1-3.fc38.ppc64le
libfdisk-2.38.1-3.fc38.ppc64le
libunistring-1.0-2.fc37.ppc64le
nettle-3.8-2.fc37.ppc64le
lz4-libs-1.9.3-5.fc37.ppc64le
libpsl-0.21.1-6.fc37.ppc64le
pam-1.5.2-15.fc38.ppc64le
libsmartcols-2.38.1-3.fc38.ppc64le
libcap-2.48-5.fc37.ppc64le
gmp-6.2.1-3.fc37.ppc64le
libpkgconf-1.8.0-3.fc37.ppc64le
coreutils-common-9.1-8.fc38.ppc64le
pkgconf-1.8.0-3.fc37.ppc64le
unzip-6.0-58.fc38.ppc64le
fedora-release-identity-basic-38-0.6.noarch
pcre2-syntax-10.40-1.fc37.1.noarch
bzip2-1.0.8-12.fc37.ppc64le
libstdc++-13.0.0-0.4.fc38.ppc64le
gzip-1.12-2.fc37.ppc64le
mpfr-4.1.1-2.fc38.ppc64le
readline-8.2-2.fc38.ppc64le
pam-libs-1.5.2-15.fc38.ppc64le
bzip2-libs-1.0.8-12.fc37.ppc64le
libselinux-3.4-6.fc38.ppc64le
kernel-srpm-macros-1.0-15.fc37.noarch
gpg-pubkey-eb10b464-6202d9c6
libidn2-2.3.4-1.fc38.ppc64le
libzstd-1.5.2-3.fc37.ppc64le
nim-srpm-macros-3-7.fc37.noarch
file-5.42-4.fc37.ppc64le
package-notes-srpm-macros-0.5-6.fc38.noarch
libtirpc-1.3.3-0.fc37.ppc64le
elfutils-libs-0.188-3.fc38.ppc64le
librtas-2.0.3-1.fc38.ppc64le
audit-libs-3.0.9-1.fc38.ppc64le
ncurses-libs-6.3-5.20221126.fc38.ppc64le
jansson-2.13.1-5.fc37.ppc64le
cpio-2.13-13.fc38.ppc64le
libxml2-2.10.3-2.fc38.ppc64le
libuuid-2.38.1-3.fc38.ppc64le
binutils-gold-2.39-6.fc38.ppc64le
fedora-repos-38-0.3.noarch
ghc-srpm-macros-1.5.0-7.fc37.noarch
rpm-4.18.0-8.fc38.ppc64le
fpc-srpm-macros-1.3-6.fc37.noarch
libpwquality-1.4.4-11.fc37.ppc64le
pkgconf-m4-1.8.0-3.fc37.noarch
binutils-2.39-6.fc38.ppc64le
openblas-srpm-macros-2-12.fc37.noarch
glibc-minimal-langpack-2.36.9000-18.fc38.ppc64le
libcom_err-1.46.5-3.fc37.ppc64le
libarchive-3.6.1-3.fc38.ppc64le
rpm-build-4.18.0-8.fc38.ppc64le
shadow-utils-4.13-3.fc38.ppc64le
ed-1.18-2.fc37.ppc64le
dwz-0.15-1.fc38.ppc64le
krb5-libs-1.20.1-3.fc38.ppc64le
libffi-3.4.4-1.fc38.ppc64le
libsigsegv-2.14-3.fc37.ppc64le
fedora-release-38-0.6.noarch
libgcc-13.0.0-0.4.fc38.ppc64le
ncurses-base-6.3-5.20221126.fc38.noarch
libssh-config-0.10.4-2.fc38.noarch
libacl-2.3.1-4.fc38.ppc64le
openldap-2.6.3-1.fc38.ppc64le
gnat-srpm-macros-4-16.fc37.noarch
xxhash-libs-0.8.1-3.fc37.ppc64le
libmount-2.38.1-3.fc38.ppc64le
gawk-5.1.1-4.fc37.ppc64le
fonts-srpm-macros-2.0.5-10.fc38.noarch
fedora-release-common-38-0.6.noarch
zip-3.0-35.fc38.ppc64le
cyrus-sasl-lib-2.1.28-8.fc38.ppc64le
elfutils-debuginfod-client-0.188-3.fc38.ppc64le
libgomp-13.0.0-0.4.fc38.ppc64le
libutempter-1.2.1-7.fc37.ppc64le
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1658275200
Wrote: /builddir/build/SRPMS/bowtie2-2.4.1-6.fc38.src.rpm
Finish: rpmbuild -bs
cp: ‘var/lib/mock/fedora-rawhide-ppc64le-1671784311.816071/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-ppc64le-1671784311.816071/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-ppc64le-1671784311.816071/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-ppc64le-1671784311.816071/root/var/log/dnf.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-1iufpb2a/bowtie2/bowtie2.spec) Config(child) 1 minutes 18 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running (timeout=115200): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/bowtie2-2.4.1-6.fc38.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1671784311.816071 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)...
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/results/bowtie2-2.4.1-6.fc38.src.rpm) Config(fedora-rawhide-ppc64le)
Start: clean chroot
Finish: clean chroot
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1671784311.816071/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1671784311.816071/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1671784311.816071/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
Mock Version: 3.5
INFO: Mock Version: 3.5
Start: dnf update
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 11 kB/s | 3.0 kB 00:00
Additional repo https_jakub_fedorapeople_org_fe 9.5 kB/s | 3.0 kB 00:00
fedora 71 kB/s | 6.7 kB 00:00
Dependencies resolved.
Nothing to do.
Complete!
Finish: dnf update
Finish: chroot init
Start: build phase for bowtie2-2.4.1-6.fc38.src.rpm
Start: build setup for bowtie2-2.4.1-6.fc38.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1658275200
Wrote: /builddir/build/SRPMS/bowtie2-2.4.1-6.fc38.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository 11 kB/s | 3.0 kB 00:00
Additional repo https_jakub_fedorapeople_org_fe 9.5 kB/s | 3.0 kB 00:00
fedora 24 kB/s | 6.7 kB 00:00
Dependencies resolved.
=================================================================================================================
Package Arch Version Repository Size
=================================================================================================================
Installing:
gcc-c++ ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 12 M
help2man noarch 1.49.3-1.fc38 fedora 228 k
libasan ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 477 k
libubsan ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 234 k
make ppc64le 1:4.3-11.fc37 fedora 554 k
perl-Clone ppc64le 0.46-1.fc38 fedora 23 k
perl-File-Which noarch 1.27-6.fc37 fedora 22 k
perl-FindBin noarch 1.53-492.fc38 fedora 17 k
perl-Sys-Hostname ppc64le 1.24-492.fc38 fedora 20 k
perl-Test-Deep noarch 1.130-9.fc37 fedora 69 k
perl-generators noarch 1.15-1.fc38 fedora 16 k
perl-interpreter ppc64le 4:5.36.0-492.fc38 fedora 75 k
perl-lib ppc64le 0.65-492.fc38 fedora 18 k
python3 ppc64le 3.11.1-1.fc38 fedora 27 k
simde-devel ppc64le 0.7.3-1.git3378ab3.fc35 fedora 437 k
zlib-devel ppc64le 1.2.13-1.fc38 fedora 45 k
Installing dependencies:
annobin-docs noarch 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 93 k
annobin-plugin-gcc ppc64le 10.99-1.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 890 k
cpp ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 9.8 M
expat ppc64le 2.5.0-1.fc38 fedora 117 k
gc ppc64le 8.2.2-1.fc38 fedora 121 k
gcc ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 30 M
gcc-plugin-annobin ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 32 k
glibc-devel ppc64le 2.36.9000-18.fc38 fedora 546 k
groff-base ppc64le 1.22.4-10.fc37 fedora 1.1 M
guile22 ppc64le 2.2.7-6.fc37 fedora 6.6 M
hedley-devel ppc64le 15-10.fc37 fedora 21 k
kernel-headers ppc64le 6.1.0-1.fc38 fedora 1.5 M
libatomic ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 19 k
libb2 ppc64le 0.98.1-7.fc37 fedora 26 k
libmpc ppc64le 1.2.1-5.fc37 fedora 85 k
libstdc++-devel ppc64le 13.0.0-0.4.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 2.4 M
libtool-ltdl ppc64le 2.4.7-3.0.1.fc38 https_jakub_fedorapeople_org_fedora_gcc13_arch 41 k
libxcrypt-devel ppc64le 4.4.33-5.fc38 fedora 30 k
mpdecimal ppc64le 2.5.1-4.fc37 fedora 117 k
ncurses ppc64le 6.3-5.20221126.fc38 fedora 421 k
perl-AutoLoader noarch 5.74-492.fc38 fedora 24 k
perl-B ppc64le 1.83-492.fc38 fedora 188 k
perl-Carp noarch 1.52-489.fc37 fedora 29 k
perl-Class-Struct noarch 0.66-492.fc38 fedora 25 k
perl-Data-Dumper ppc64le 2.184-490.fc37 fedora 58 k
perl-DynaLoader ppc64le 1.52-492.fc38 fedora 29 k
perl-Encode ppc64le 4:3.19-492.fc38 fedora 1.7 M
perl-Errno ppc64le 1.36-492.fc38 fedora 18 k
perl-Exporter noarch 5.77-489.fc37 fedora 31 k
perl-Fcntl ppc64le 1.15-492.fc38 fedora 24 k
perl-Fedora-VSP noarch 0.001-30.fc38 fedora 23 k
perl-File-Basename noarch 2.85-492.fc38 fedora 20 k
perl-File-Path noarch 2.18-489.fc37 fedora 35 k
perl-File-Temp noarch 1:0.231.100-489.fc37 fedora 59 k
perl-File-stat noarch 1.12-492.fc38 fedora 20 k
perl-Getopt-Long noarch 1:2.54-1.fc38 fedora 60 k
perl-Getopt-Std noarch 1.13-492.fc38 fedora 19 k
perl-HTTP-Tiny noarch 0.082-1.fc37 fedora 55 k
perl-IO ppc64le 1.50-492.fc38 fedora 95 k
perl-IPC-Open3 noarch 1.22-492.fc38 fedora 26 k
perl-Importer noarch 0.026-8.fc38 fedora 39 k
perl-JSON-PP noarch 1:4.12-1.fc38 fedora 68 k
perl-MIME-Base64 ppc64le 3.16-489.fc37 fedora 31 k
perl-Math-BigInt noarch 1:1.9998.37-2.fc37 fedora 206 k
perl-Math-BigRat noarch 0.2624-2.fc37 fedora 42 k
perl-Math-Complex noarch 1.59-492.fc38 fedora 50 k
perl-Object-HashBase noarch 0.009-11.fc38 fedora 25 k
perl-POSIX ppc64le 2.03-492.fc38 fedora 121 k
perl-PathTools ppc64le 3.84-489.fc37 fedora 90 k
perl-Pod-Escapes noarch 1:1.07-489.fc37 fedora 20 k
perl-Pod-Perldoc noarch 3.28.01-490.fc37 fedora 90 k
perl-Pod-Simple noarch 1:3.43-490.fc37 fedora 225 k
perl-Pod-Usage noarch 4:2.03-3.fc37 fedora 40 k
perl-Scalar-List-Utils ppc64le 5:1.63-489.fc38 fedora 76 k
perl-SelectSaver noarch 1.02-492.fc38 fedora 15 k
perl-Socket ppc64le 4:2.036-1.fc38 fedora 56 k
perl-Storable ppc64le 1:3.26-489.fc37 fedora 101 k
perl-Symbol noarch 1.09-492.fc38 fedora 17 k
perl-Term-ANSIColor noarch 5.01-490.fc37 fedora 48 k
perl-Term-Cap noarch 1.17-489.fc37 fedora 22 k
perl-Term-Table noarch 0.016-5.fc38 fedora 34 k
perl-Test-Simple noarch 3:1.302191-2.fc37 fedora 592 k
perl-Text-ParseWords noarch 3.31-489.fc37 fedora 16 k
perl-Text-Tabs+Wrap noarch 2021.0814-489.fc37 fedora 22 k
perl-Time-HiRes ppc64le 4:1.9770-489.fc37 fedora 58 k
perl-Time-Local noarch 2:1.300-489.fc37 fedora 33 k
perl-base noarch 2.27-492.fc38 fedora 19 k
perl-constant noarch 1.33-490.fc37 fedora 23 k
perl-if noarch 0.61.000-492.fc38 fedora 17 k
perl-libs ppc64le 4:5.36.0-492.fc38 fedora 2.3 M
perl-macros noarch 4:5.36.0-492.fc38 fedora 14 k
perl-mro ppc64le 1.26-492.fc38 fedora 32 k
perl-overload noarch 1.35-492.fc38 fedora 49 k
perl-overloading noarch 0.02-492.fc38 fedora 16 k
perl-parent noarch 1:0.239-1.fc38 fedora 14 k
perl-podlators noarch 1:5.00-1.fc38 fedora 127 k
perl-vars noarch 1.05-492.fc38 fedora 16 k
python-pip-wheel noarch 22.3.1-1.fc38 fedora 1.4 M
python-setuptools-wheel noarch 65.5.1-1.fc38 fedora 715 k
python3-libs ppc64le 3.11.1-1.fc38 fedora 9.7 M
Transaction Summary
=================================================================================================================
Install 96 Packages
Total size: 87 M
Total download size: 2.0 M
Installed size: 327 M
Downloading Packages:
[SKIPPED] annobin-docs-10.99-1.0.1.fc38.noarch.rpm: Already downloaded
[SKIPPED] annobin-plugin-gcc-10.99-1.0.1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] cpp-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
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[SKIPPED] gcc-c++-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gcc-plugin-annobin-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libasan-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libatomic-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libstdc++-devel-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libtool-ltdl-2.4.7-3.0.1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libubsan-13.0.0-0.4.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] expat-2.5.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] gc-8.2.2-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] glibc-devel-2.36.9000-18.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] groff-base-1.22.4-10.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] guile22-2.2.7-6.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] kernel-headers-6.1.0-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] libb2-0.98.1-7.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libmpc-1.2.1-5.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] libxcrypt-devel-4.4.33-5.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] make-4.3-11.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] mpdecimal-2.5.1-4.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] ncurses-6.3-5.20221126.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-AutoLoader-5.74-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-B-1.83-492.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Carp-1.52-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Class-Struct-0.66-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Clone-0.46-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Data-Dumper-2.184-490.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] perl-DynaLoader-1.52-492.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Encode-3.19-492.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Errno-1.36-492.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Exporter-5.77-489.fc37.noarch.rpm: Already downloaded
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[SKIPPED] perl-File-Basename-2.85-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-File-Path-2.18-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-File-Temp-0.231.100-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-File-stat-1.12-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Getopt-Long-2.54-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Getopt-Std-1.13-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-HTTP-Tiny-0.082-1.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-IO-1.50-492.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-IPC-Open3-1.22-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-MIME-Base64-3.16-489.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] perl-POSIX-2.03-492.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-PathTools-3.84-489.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Pod-Escapes-1.07-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Pod-Perldoc-3.28.01-490.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Pod-Simple-3.43-490.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Pod-Usage-2.03-3.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Scalar-List-Utils-1.63-489.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-SelectSaver-1.02-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Socket-2.036-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Storable-3.26-489.fc37.ppc64le.rpm: Already downloaded
[SKIPPED] perl-Symbol-1.09-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-Term-ANSIColor-5.01-490.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Term-Cap-1.17-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Text-ParseWords-3.31-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-Time-Local-1.300-489.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-base-2.27-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-constant-1.33-490.fc37.noarch.rpm: Already downloaded
[SKIPPED] perl-if-0.61.000-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-interpreter-5.36.0-492.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-libs-5.36.0-492.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-mro-1.26-492.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] perl-overload-1.35-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-overloading-0.02-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-parent-0.239-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-podlators-5.00-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] perl-vars-1.05-492.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-pip-wheel-22.3.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python-setuptools-wheel-65.5.1-1.fc38.noarch.rpm: Already downloaded
[SKIPPED] python3-3.11.1-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] python3-libs-3.11.1-1.fc38.ppc64le.rpm: Already downloaded
[SKIPPED] zlib-devel-1.2.13-1.fc38.ppc64le.rpm: Already downloaded
(77/96): hedley-devel-15-10.fc37.ppc64le.rpm 50 kB/s | 21 kB 00:00
(78/96): perl-Fedora-VSP-0.001-30.fc38.noarch.r 55 kB/s | 23 kB 00:00
(79/96): perl-File-Which-1.27-6.fc37.noarch.rpm 469 kB/s | 22 kB 00:00
(80/96): perl-FindBin-1.53-492.fc38.noarch.rpm 212 kB/s | 17 kB 00:00
(81/96): perl-Importer-0.026-8.fc38.noarch.rpm 825 kB/s | 39 kB 00:00
(82/96): help2man-1.49.3-1.fc38.noarch.rpm 436 kB/s | 228 kB 00:00
(83/96): perl-JSON-PP-4.12-1.fc38.noarch.rpm 1.4 MB/s | 68 kB 00:00
(84/96): perl-Math-BigInt-1.9998.37-2.fc37.noar 1.7 MB/s | 206 kB 00:00
(85/96): perl-Math-BigRat-0.2624-2.fc37.noarch. 413 kB/s | 42 kB 00:00
(86/96): perl-Math-Complex-1.59-492.fc38.noarch 465 kB/s | 50 kB 00:00
(87/96): perl-Object-HashBase-0.009-11.fc38.noa 350 kB/s | 25 kB 00:00
(88/96): perl-Sys-Hostname-1.24-492.fc38.ppc64l 197 kB/s | 20 kB 00:00
(89/96): perl-Term-Table-0.016-5.fc38.noarch.rp 335 kB/s | 34 kB 00:00
(90/96): perl-Test-Deep-1.130-9.fc37.noarch.rpm 685 kB/s | 69 kB 00:00
(91/96): perl-Time-HiRes-1.9770-489.fc37.ppc64l 703 kB/s | 58 kB 00:00
(92/96): perl-Test-Simple-1.302191-2.fc37.noarc 4.1 MB/s | 592 kB 00:00
(93/96): perl-generators-1.15-1.fc38.noarch.rpm 169 kB/s | 16 kB 00:00
(94/96): perl-lib-0.65-492.fc38.ppc64le.rpm 260 kB/s | 18 kB 00:00
(95/96): perl-macros-5.36.0-492.fc38.noarch.rpm 179 kB/s | 14 kB 00:00
(96/96): simde-devel-0.7.3-1.git3378ab3.fc35.pp 3.3 MB/s | 437 kB 00:00
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Total 1.2 MB/s | 2.0 MB 00:01
Running transaction check
Transaction check succeeded.
Running transaction test
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Running transaction
Preparing : 1/1
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Verifying : mpdecimal-2.5.1-4.fc37.ppc64le 24/96
Verifying : ncurses-6.3-5.20221126.fc38.ppc64le 25/96
Verifying : perl-AutoLoader-5.74-492.fc38.noarch 26/96
Verifying : perl-B-1.83-492.fc38.ppc64le 27/96
Verifying : perl-Carp-1.52-489.fc37.noarch 28/96
Verifying : perl-Class-Struct-0.66-492.fc38.noarch 29/96
Verifying : perl-Clone-0.46-1.fc38.ppc64le 30/96
Verifying : perl-Data-Dumper-2.184-490.fc37.ppc64le 31/96
Verifying : perl-DynaLoader-1.52-492.fc38.ppc64le 32/96
Verifying : perl-Encode-4:3.19-492.fc38.ppc64le 33/96
Verifying : perl-Errno-1.36-492.fc38.ppc64le 34/96
Verifying : perl-Exporter-5.77-489.fc37.noarch 35/96
Verifying : perl-Fcntl-1.15-492.fc38.ppc64le 36/96
Verifying : perl-Fedora-VSP-0.001-30.fc38.noarch 37/96
Verifying : perl-File-Basename-2.85-492.fc38.noarch 38/96
Verifying : perl-File-Path-2.18-489.fc37.noarch 39/96
Verifying : perl-File-Temp-1:0.231.100-489.fc37.noarch 40/96
Verifying : perl-File-Which-1.27-6.fc37.noarch 41/96
Verifying : perl-File-stat-1.12-492.fc38.noarch 42/96
Verifying : perl-FindBin-1.53-492.fc38.noarch 43/96
Verifying : perl-Getopt-Long-1:2.54-1.fc38.noarch 44/96
Verifying : perl-Getopt-Std-1.13-492.fc38.noarch 45/96
Verifying : perl-HTTP-Tiny-0.082-1.fc37.noarch 46/96
Verifying : perl-IO-1.50-492.fc38.ppc64le 47/96
Verifying : perl-IPC-Open3-1.22-492.fc38.noarch 48/96
Verifying : perl-Importer-0.026-8.fc38.noarch 49/96
Verifying : perl-JSON-PP-1:4.12-1.fc38.noarch 50/96
Verifying : perl-MIME-Base64-3.16-489.fc37.ppc64le 51/96
Verifying : perl-Math-BigInt-1:1.9998.37-2.fc37.noarch 52/96
Verifying : perl-Math-BigRat-0.2624-2.fc37.noarch 53/96
Verifying : perl-Math-Complex-1.59-492.fc38.noarch 54/96
Verifying : perl-Object-HashBase-0.009-11.fc38.noarch 55/96
Verifying : perl-POSIX-2.03-492.fc38.ppc64le 56/96
Verifying : perl-PathTools-3.84-489.fc37.ppc64le 57/96
Verifying : perl-Pod-Escapes-1:1.07-489.fc37.noarch 58/96
Verifying : perl-Pod-Perldoc-3.28.01-490.fc37.noarch 59/96
Verifying : perl-Pod-Simple-1:3.43-490.fc37.noarch 60/96
Verifying : perl-Pod-Usage-4:2.03-3.fc37.noarch 61/96
Verifying : perl-Scalar-List-Utils-5:1.63-489.fc38.ppc64le 62/96
Verifying : perl-SelectSaver-1.02-492.fc38.noarch 63/96
Verifying : perl-Socket-4:2.036-1.fc38.ppc64le 64/96
Verifying : perl-Storable-1:3.26-489.fc37.ppc64le 65/96
Verifying : perl-Symbol-1.09-492.fc38.noarch 66/96
Verifying : perl-Sys-Hostname-1.24-492.fc38.ppc64le 67/96
Verifying : perl-Term-ANSIColor-5.01-490.fc37.noarch 68/96
Verifying : perl-Term-Cap-1.17-489.fc37.noarch 69/96
Verifying : perl-Term-Table-0.016-5.fc38.noarch 70/96
Verifying : perl-Test-Deep-1.130-9.fc37.noarch 71/96
Verifying : perl-Test-Simple-3:1.302191-2.fc37.noarch 72/96
Verifying : perl-Text-ParseWords-3.31-489.fc37.noarch 73/96
Verifying : perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch 74/96
Verifying : perl-Time-HiRes-4:1.9770-489.fc37.ppc64le 75/96
Verifying : perl-Time-Local-2:1.300-489.fc37.noarch 76/96
Verifying : perl-base-2.27-492.fc38.noarch 77/96
Verifying : perl-constant-1.33-490.fc37.noarch 78/96
Verifying : perl-generators-1.15-1.fc38.noarch 79/96
Verifying : perl-if-0.61.000-492.fc38.noarch 80/96
Verifying : perl-interpreter-4:5.36.0-492.fc38.ppc64le 81/96
Verifying : perl-lib-0.65-492.fc38.ppc64le 82/96
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Verifying : perl-overload-1.35-492.fc38.noarch 86/96
Verifying : perl-overloading-0.02-492.fc38.noarch 87/96
Verifying : perl-parent-1:0.239-1.fc38.noarch 88/96
Verifying : perl-podlators-1:5.00-1.fc38.noarch 89/96
Verifying : perl-vars-1.05-492.fc38.noarch 90/96
Verifying : python-pip-wheel-22.3.1-1.fc38.noarch 91/96
Verifying : python-setuptools-wheel-65.5.1-1.fc38.noarch 92/96
Verifying : python3-3.11.1-1.fc38.ppc64le 93/96
Verifying : python3-libs-3.11.1-1.fc38.ppc64le 94/96
Verifying : simde-devel-0.7.3-1.git3378ab3.fc35.ppc64le 95/96
Verifying : zlib-devel-1.2.13-1.fc38.ppc64le 96/96
Installed:
annobin-docs-10.99-1.0.1.fc38.noarch
annobin-plugin-gcc-10.99-1.0.1.fc38.ppc64le
cpp-13.0.0-0.4.fc38.ppc64le
expat-2.5.0-1.fc38.ppc64le
gc-8.2.2-1.fc38.ppc64le
gcc-13.0.0-0.4.fc38.ppc64le
gcc-c++-13.0.0-0.4.fc38.ppc64le
gcc-plugin-annobin-13.0.0-0.4.fc38.ppc64le
glibc-devel-2.36.9000-18.fc38.ppc64le
groff-base-1.22.4-10.fc37.ppc64le
guile22-2.2.7-6.fc37.ppc64le
hedley-devel-15-10.fc37.ppc64le
help2man-1.49.3-1.fc38.noarch
kernel-headers-6.1.0-1.fc38.ppc64le
libasan-13.0.0-0.4.fc38.ppc64le
libatomic-13.0.0-0.4.fc38.ppc64le
libb2-0.98.1-7.fc37.ppc64le
libmpc-1.2.1-5.fc37.ppc64le
libstdc++-devel-13.0.0-0.4.fc38.ppc64le
libtool-ltdl-2.4.7-3.0.1.fc38.ppc64le
libubsan-13.0.0-0.4.fc38.ppc64le
libxcrypt-devel-4.4.33-5.fc38.ppc64le
make-1:4.3-11.fc37.ppc64le
mpdecimal-2.5.1-4.fc37.ppc64le
ncurses-6.3-5.20221126.fc38.ppc64le
perl-AutoLoader-5.74-492.fc38.noarch
perl-B-1.83-492.fc38.ppc64le
perl-Carp-1.52-489.fc37.noarch
perl-Class-Struct-0.66-492.fc38.noarch
perl-Clone-0.46-1.fc38.ppc64le
perl-Data-Dumper-2.184-490.fc37.ppc64le
perl-DynaLoader-1.52-492.fc38.ppc64le
perl-Encode-4:3.19-492.fc38.ppc64le
perl-Errno-1.36-492.fc38.ppc64le
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perl-Getopt-Long-1:2.54-1.fc38.noarch
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perl-IPC-Open3-1.22-492.fc38.noarch
perl-Importer-0.026-8.fc38.noarch
perl-JSON-PP-1:4.12-1.fc38.noarch
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perl-Symbol-1.09-492.fc38.noarch
perl-Sys-Hostname-1.24-492.fc38.ppc64le
perl-Term-ANSIColor-5.01-490.fc37.noarch
perl-Term-Cap-1.17-489.fc37.noarch
perl-Term-Table-0.016-5.fc38.noarch
perl-Test-Deep-1.130-9.fc37.noarch
perl-Test-Simple-3:1.302191-2.fc37.noarch
perl-Text-ParseWords-3.31-489.fc37.noarch
perl-Text-Tabs+Wrap-2021.0814-489.fc37.noarch
perl-Time-HiRes-4:1.9770-489.fc37.ppc64le
perl-Time-Local-2:1.300-489.fc37.noarch
perl-base-2.27-492.fc38.noarch
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perl-generators-1.15-1.fc38.noarch
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perl-lib-0.65-492.fc38.ppc64le
perl-libs-4:5.36.0-492.fc38.ppc64le
perl-macros-4:5.36.0-492.fc38.noarch
perl-mro-1.26-492.fc38.ppc64le
perl-overload-1.35-492.fc38.noarch
perl-overloading-0.02-492.fc38.noarch
perl-parent-1:0.239-1.fc38.noarch
perl-podlators-1:5.00-1.fc38.noarch
perl-vars-1.05-492.fc38.noarch
python-pip-wheel-22.3.1-1.fc38.noarch
python-setuptools-wheel-65.5.1-1.fc38.noarch
python3-3.11.1-1.fc38.ppc64le
python3-libs-3.11.1-1.fc38.ppc64le
simde-devel-0.7.3-1.git3378ab3.fc35.ppc64le
zlib-devel-1.2.13-1.fc38.ppc64le
Complete!
Finish: build setup for bowtie2-2.4.1-6.fc38.src.rpm
Start: rpmbuild bowtie2-2.4.1-6.fc38.src.rpm
Building target platforms: ppc64le
Building for target ppc64le
setting SOURCE_DATE_EPOCH=1658275200
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.1u5a7o
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf bowtie2-2.4.1
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/v2.4.1.tar.gz
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bowtie2-2.4.1
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ /usr/lib/rpm/rpmuncompress /builddir/build/SOURCES/bowtie2-makefile-cxxflags.patch
+ /usr/bin/patch -s --fuzz=0 --no-backup-if-mismatch -f
+ rm -rf third_party
+ sed -e 's/“/"/g' -e 's/â€/"/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.nKW69b
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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,-D_FORTIFY_SOURCE=2 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bowtie2-2.4.1
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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,-D_FORTIFY_SOURCE=2 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ 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,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -Wall \
-Ithird_party/simde -I . \
-o bowtie2-inspect-s bt2_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lz -lpthread
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,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-Ithird_party/simde \
-o bowtie2-build-l bt2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lz -lpthread
In file included from bt2_idx.h:46,
from bt2_build.cpp:28:
In function 'fastaRefReadAppend<S2bDnaString>(FileBuf&, bool, S2bDnaString&, unsigned long&, RefReadInParams&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)RefRecord',
inlined from 'Ebwt::joinToDisk<S2bDnaString>(EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned long, RefReadInParams const&, S2bDnaString&, std::basic_ostream<char, std::char_traits<char> >&, std::basic_ostream<char, std::char_traits<char> >&)void [clone .isra.0]' at bt2_idx.h:2633:38:
ref_read.h:295:49: warning: array subscript -1 is below array bounds of 'uint8_t[<unknown>]' [-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<S2bDnaString>(EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned long, RefReadInParams const&, S2bDnaString&, std::basic_ostream<char, std::char_traits<char> >&, std::basic_ostream<char, std::char_traits<char> >&)void [clone .isra.0]':
alphabet.h:36:16: note: while referencing 'asc2dnacat'
36 | extern uint8_t asc2dnacat[];
| ^~~~~~~~~~
ref_read.h: In function 'fastaRefReadAppend<SString<char> >(FileBuf&, bool, SString<char>&, unsigned long&, RefReadInParams&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)RefRecord':
ref_read.h:295:49: warning: array subscript -1 is below array bounds of 'uint8_t[<unknown>]' [-Warray-bounds=]
295 | if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A';
| ~~~~~~~~~~~~^
alphabet.h:36:16: note: while referencing 'asc2dnacat'
36 | extern uint8_t asc2dnacat[];
| ^~~~~~~~~~
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,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
-Ithird_party/simde \
-o bowtie2-build-s bt2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp bowtie_build_main.cpp \
-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lz -lpthread
In file included from bt2_idx.h:46,
from bt2_build.cpp:28:
In function 'fastaRefReadAppend<S2bDnaString>(FileBuf&, bool, S2bDnaString&, unsigned int&, RefReadInParams&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)RefRecord',
inlined from 'Ebwt::joinToDisk<S2bDnaString>(EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned int, RefReadInParams const&, S2bDnaString&, std::basic_ostream<char, std::char_traits<char> >&, std::basic_ostream<char, std::char_traits<char> >&)void [clone .isra.0]' at bt2_idx.h:2633:38:
ref_read.h:295:49: warning: array subscript -1 is below array bounds of 'uint8_t[<unknown>]' [-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<S2bDnaString>(EList<FileBuf*, 128>&, EList<RefRecord, 128>&, unsigned int, RefReadInParams const&, S2bDnaString&, std::basic_ostream<char, std::char_traits<char> >&, std::basic_ostream<char, std::char_traits<char> >&)void [clone .isra.0]':
alphabet.h:36:16: note: while referencing 'asc2dnacat'
36 | extern uint8_t asc2dnacat[];
| ^~~~~~~~~~
ref_read.h: In function 'fastaRefReadAppend<SString<char> >(FileBuf&, bool, SString<char>&, unsigned int&, RefReadInParams&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*)RefRecord':
ref_read.h:295:49: warning: array subscript -1 is below array bounds of 'uint8_t[<unknown>]' [-Warray-bounds=]
295 | if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A';
| ~~~~~~~~~~~~^
alphabet.h:36:16: note: while referencing 'asc2dnacat'
36 | extern uint8_t asc2dnacat[];
| ^~~~~~~~~~
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,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_INSPECT_MAIN -DBOWTIE_64BIT_INDEX -Wall \
-Ithird_party/simde -I . \
-o bowtie2-inspect-l bt2_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lz -lpthread
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,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DNDEBUG -Wall \
-Ithird_party/simde \
-o bowtie2-align-s bt2_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lz -lpthread
In file included from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:31,
from blockwise_sa.h:35,
from bt2_idx.h:42,
from bt2_search.cpp:40:
ds.h: In instantiation of 'EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]':
ds.h:973:12: required from 'void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:958:3: required from 'void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:569:4: required from 'void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
aligner_seed2.h:482:25: required from here
ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<DescentRedundancyKey, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/string:51,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from bt2_search.cpp:21:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair<DescentRedundancyKey, long int>' declared here
187 | struct pair
| ^~~~
In member function 'std::basic_ostream<char, std::char_traits<char> >::operator<<(void const*)',
inlined from 'read_dir(char const*, int*)' at bt2_search.cpp:4610:53,
inlined from 'steal_threads<tthread::thread>(int, int, EList<int, 128>&, EList<tthread::thread*, 128>&)void' at bt2_search.cpp:4626:27,
inlined from 'thread_monitor<tthread::thread>(int, int, EList<int, 128>&, EList<tthread::thread*, 128>&)void' at bt2_search.cpp:4647:16,
inlined from 'multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)' at bt2_search.cpp:4782:18:
/usr/include/c++/13/ostream:293:25: warning: pointer may be used after 'closedir' [-Wuse-after-free]
293 | { return _M_insert(__p); }
| ~~~~~~~~~^~~~~
In function 'read_dir(char const*, int*)',
inlined from 'steal_threads<tthread::thread>(int, int, EList<int, 128>&, EList<tthread::thread*, 128>&)void' at bt2_search.cpp:4626:27,
inlined from 'thread_monitor<tthread::thread>(int, int, EList<int, 128>&, EList<tthread::thread*, 128>&)void' at bt2_search.cpp:4647:16,
inlined from 'multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)' at bt2_search.cpp:4782:18:
bt2_search.cpp:4608:20: note: call to 'closedir' here
4608 | if(closedir(dir) != 0) {
| ~~~~~~~~^~~~~
In file included from random_util.h:25,
from aligner_seed2.h:101,
from aligner_seed2.cpp:22:
ds.h: In instantiation of 'EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]':
ds.h:973:12: required from 'void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:958:3: required from 'void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:569:4: required from 'void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
aligner_seed2.h:482:25: required from here
ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<DescentRedundancyKey, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/bits/specfun.h:43,
from /usr/include/c++/13/cmath:3716,
from /usr/include/c++/13/math.h:36,
from aligner_seed2.h:97:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair<DescentRedundancyKey, long int>' declared here
187 | struct pair
| ^~~~
In file included from sse_wrap.h:31,
from aligner_sw.h:73,
from aligner_swsse_loc_i16.cpp:56:
aligner_swsse_loc_i16.cpp: In member function 'TAlScore SwAligner::alignGatherLoc16(int&, bool)':
aligner_swsse_loc_i16.cpp:415:49: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
415 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ~~~~~~~~~~~~~~^~
aligner_swsse_loc_i16.cpp:415:15: note: in expansion of macro '_mm_slli_epi16'
415 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ^~~~~~~~~~~~~~
aligner_swsse_loc_i16.cpp:497:55: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
497 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ~~~~~~~~~~~~~~^~
aligner_swsse_loc_i16.cpp:497:22: note: in expansion of macro '_mm_slli_epi16'
497 | vf = _mm_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:1045:49: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
1045 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ~~~~~~~~~~~~~~^~
aligner_swsse_loc_i16.cpp:1045:15: note: in expansion of macro '_mm_slli_epi16'
1045 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ^~~~~~~~~~~~~~
aligner_swsse_loc_i16.cpp:1123:55: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
1123 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ~~~~~~~~~~~~~~^~
aligner_swsse_loc_i16.cpp:1123:22: note: in expansion of macro '_mm_slli_epi16'
1123 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ^~~~~~~~~~~~~~
In file included from sse_wrap.h:31,
from aligner_sw.h:73,
from aligner_swsse_ee_i16.cpp:56:
aligner_swsse_ee_i16.cpp: In member function 'TAlScore SwAligner::alignGatherEE16(int&, bool)':
aligner_swsse_ee_i16.cpp:403:49: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
403 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ~~~~~~~~~~~~~~^~
aligner_swsse_ee_i16.cpp:403:15: note: in expansion of macro '_mm_slli_epi16'
403 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ^~~~~~~~~~~~~~
aligner_swsse_ee_i16.cpp:478:55: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
478 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ~~~~~~~~~~~~~~^~
aligner_swsse_ee_i16.cpp:478:22: note: in expansion of macro '_mm_slli_epi16'
478 | vf = _mm_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:871:49: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
871 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ~~~~~~~~~~~~~~^~
aligner_swsse_ee_i16.cpp:871:15: note: in expansion of macro '_mm_slli_epi16'
871 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ^~~~~~~~~~~~~~
aligner_swsse_ee_i16.cpp:952:55: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
952 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ~~~~~~~~~~~~~~^~
aligner_swsse_ee_i16.cpp:952:22: note: in expansion of macro '_mm_slli_epi16'
952 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ^~~~~~~~~~~~~~
In file included from random_util.h:25,
from aligner_seed2.h:101,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
ds.h: In instantiation of 'EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]':
ds.h:973:12: required from 'void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:958:3: required from 'void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:569:4: required from 'void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
aligner_seed2.h:482:25: required from here
ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<DescentRedundancyKey, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/bits/specfun.h:43,
from /usr/include/c++/13/cmath:3716,
from /usr/include/c++/13/math.h:36,
from aligner_seed2.h:97:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair<DescentRedundancyKey, long int>' declared here
187 | struct pair
| ^~~~
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopyExact' at ds.h:965:7,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'push_back' at ds.h:496:29,
inlined from 'setupPatternComposer.constprop' at pat.cpp:309:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'setupPatternComposer.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopyExact' at ds.h:965:7,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'push_back' at ds.h:496:29,
inlined from 'setupPatternComposer.constprop' at pat.cpp:346:20:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'setupPatternComposer.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopyExact' at ds.h:965:7,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'push_back' at ds.h:496:29,
inlined from 'setupPatternComposer.constprop' at pat.cpp:363:20:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'setupPatternComposer.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'expand' at ds.h:505:29,
inlined from 'parseFasta' at sequence_io.h:88:15:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'parseFasta':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'expand' at ds.h:505:29,
inlined from 'parseFasta' at sequence_io.h:89:14:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'parseFasta':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandNoCopyExact' at ds.h:1003:17,
inlined from 'expandNoCopy' at ds.h:992:20,
inlined from 'operator=' at ds.h:405:32,
inlined from 'operator=' at ds.h:394:15,
inlined from '__ct ' at ds.h:373:9,
inlined from '__ct_base ' at pat.h:348:3:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In member function '__ct_base ':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function '__ct ',
inlined from 'driver.constprop' at bt2_search.cpp:4923:14:
outq.h:75:81: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
75 | perThreadBuf[i] = new BTString[perThreadBufSize_];
| ^
/usr/include/c++/13/new: In function 'driver.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'expand' at ds.h:505:29,
inlined from '__ct ' at pat.cpp:564:15,
inlined from 'patsrcFromStrings' at pat.cpp:100:57:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'patsrcFromStrings':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopyExact' at ds.h:965:7,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'ensure' at ds.h:467:13,
inlined from 'advanceElement' at group_walk.h:1179:14,
inlined from 'next' at aligner_seed2.h:2203:30,
inlined from 'go' at aligner_driver.cpp:326:29,
inlined from 'multiseedSearchWorker_2p5' at bt2_search.cpp:4435:11:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'multiseedSearchWorker_2p5':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopyExact' at ds.h:965:7,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'expand' at ds.h:505:29,
inlined from 'instantiateSeeds.isra' at aligner_seed.cpp:434:15:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In member function 'instantiateSeeds.isra':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from '_ZN5EListI10Random1toNLi16EE15expandCopyExactEm.part.0' at ds.h:967:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In member function '_ZN5EListI10Random1toNLi16EE15expandCopyExactEm.part.0':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from '_ZN5EListI11GroupWalk2SI10PListSliceIjLi16384EELi16EELi128EE15expandCopyExactEm.part.0' at ds.h:967:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In member function '_ZN5EListI11GroupWalk2SI10PListSliceIjLi16384EELi16EELi128EE15expandCopyExactEm.part.0':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
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,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd\"" -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -fopenmp-simd \
-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"\"" -DBUILD_TIME="\"`date -u`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-Ithird_party/simde \
-o bowtie2-align-l bt2_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp bowtie_main.cpp \
-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -lz -lpthread
In file included from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:31,
from blockwise_sa.h:35,
from bt2_idx.h:42,
from bt2_search.cpp:40:
ds.h: In instantiation of 'EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]':
ds.h:973:12: required from 'void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:958:3: required from 'void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:569:4: required from 'void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
aligner_seed2.h:482:25: required from here
ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<DescentRedundancyKey, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/string:51,
from /usr/include/c++/13/bits/locale_classes.h:40,
from /usr/include/c++/13/bits/ios_base.h:41,
from /usr/include/c++/13/ios:44,
from /usr/include/c++/13/ostream:40,
from /usr/include/c++/13/iostream:41,
from bt2_search.cpp:21:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair<DescentRedundancyKey, long int>' declared here
187 | struct pair
| ^~~~
In member function 'std::basic_ostream<char, std::char_traits<char> >::operator<<(void const*)',
inlined from 'read_dir(char const*, int*)' at bt2_search.cpp:4610:53,
inlined from 'steal_threads<tthread::thread>(int, int, EList<int, 128>&, EList<tthread::thread*, 128>&)void' at bt2_search.cpp:4626:27,
inlined from 'thread_monitor<tthread::thread>(int, int, EList<int, 128>&, EList<tthread::thread*, 128>&)void' at bt2_search.cpp:4647:16,
inlined from 'multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)' at bt2_search.cpp:4782:18:
/usr/include/c++/13/ostream:293:25: warning: pointer may be used after 'closedir' [-Wuse-after-free]
293 | { return _M_insert(__p); }
| ~~~~~~~~~^~~~~
In function 'read_dir(char const*, int*)',
inlined from 'steal_threads<tthread::thread>(int, int, EList<int, 128>&, EList<tthread::thread*, 128>&)void' at bt2_search.cpp:4626:27,
inlined from 'thread_monitor<tthread::thread>(int, int, EList<int, 128>&, EList<tthread::thread*, 128>&)void' at bt2_search.cpp:4647:16,
inlined from 'multiseedSearch(Scoring&, PatternParams const&, PatternComposer&, AlnSink&, Ebwt&, Ebwt*, OutFileBuf*)' at bt2_search.cpp:4782:18:
bt2_search.cpp:4608:20: note: call to 'closedir' here
4608 | if(closedir(dir) != 0) {
| ~~~~~~~~^~~~~
In file included from random_util.h:25,
from aligner_seed2.h:101,
from aligner_seed2.cpp:22:
ds.h: In instantiation of 'EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]':
ds.h:973:12: required from 'void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:958:3: required from 'void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:569:4: required from 'void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
aligner_seed2.h:482:25: required from here
ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<DescentRedundancyKey, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/bits/specfun.h:43,
from /usr/include/c++/13/cmath:3716,
from /usr/include/c++/13/math.h:36,
from aligner_seed2.h:97:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair<DescentRedundancyKey, long int>' declared here
187 | struct pair
| ^~~~
In file included from sse_wrap.h:31,
from aligner_sw.h:73,
from aligner_swsse_loc_i16.cpp:56:
aligner_swsse_loc_i16.cpp: In member function 'TAlScore SwAligner::alignGatherLoc16(int&, bool)':
aligner_swsse_loc_i16.cpp:415:49: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
415 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ~~~~~~~~~~~~~~^~
aligner_swsse_loc_i16.cpp:415:15: note: in expansion of macro '_mm_slli_epi16'
415 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ^~~~~~~~~~~~~~
aligner_swsse_loc_i16.cpp:497:55: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
497 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ~~~~~~~~~~~~~~^~
aligner_swsse_loc_i16.cpp:497:22: note: in expansion of macro '_mm_slli_epi16'
497 | vf = _mm_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:1045:49: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
1045 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ~~~~~~~~~~~~~~^~
aligner_swsse_loc_i16.cpp:1045:15: note: in expansion of macro '_mm_slli_epi16'
1045 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ^~~~~~~~~~~~~~
aligner_swsse_loc_i16.cpp:1123:55: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
1123 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ~~~~~~~~~~~~~~^~
aligner_swsse_loc_i16.cpp:1123:22: note: in expansion of macro '_mm_slli_epi16'
1123 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ^~~~~~~~~~~~~~
In file included from sse_wrap.h:31,
from aligner_sw.h:73,
from aligner_swsse_ee_i16.cpp:56:
aligner_swsse_ee_i16.cpp: In member function 'TAlScore SwAligner::alignGatherEE16(int&, bool)':
aligner_swsse_ee_i16.cpp:403:49: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
403 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ~~~~~~~~~~~~~~^~
aligner_swsse_ee_i16.cpp:403:15: note: in expansion of macro '_mm_slli_epi16'
403 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ^~~~~~~~~~~~~~
aligner_swsse_ee_i16.cpp:478:55: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
478 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ~~~~~~~~~~~~~~^~
aligner_swsse_ee_i16.cpp:478:22: note: in expansion of macro '_mm_slli_epi16'
478 | vf = _mm_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:871:49: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
871 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ~~~~~~~~~~~~~~^~
aligner_swsse_ee_i16.cpp:871:15: note: in expansion of macro '_mm_slli_epi16'
871 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000
| ^~~~~~~~~~~~~~
aligner_swsse_ee_i16.cpp:952:55: warning: suggest parentheses around '-' in operand of '&' [-Wparentheses]
952 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ~~~~~~~~~~~~~~^~
aligner_swsse_ee_i16.cpp:952:22: note: in expansion of macro '_mm_slli_epi16'
952 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1);
| ^~~~~~~~~~~~~~
In file included from random_util.h:25,
from aligner_seed2.h:101,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
ds.h: In instantiation of 'EMap<K, V>& EMap<K, V>::operator=(const EMap<K, V>&) [with K = DescentRedundancyKey; V = long int]':
ds.h:973:12: required from 'void EList<T, S>::expandCopyExact(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:958:3: required from 'void EList<T, S>::expandCopy(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
ds.h:569:4: required from 'void EList<T, S>::resize(size_t) [with T = EMap<DescentRedundancyKey, long int>; int S = 8; size_t = long unsigned int]'
aligner_seed2.h:482:25: required from here
ds.h:2456:23: warning: 'void* memcpy(void*, const void*, size_t)' writing to an object of type 'struct std::pair<DescentRedundancyKey, long int>' with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
2456 | memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/bits/stl_algobase.h:64,
from /usr/include/c++/13/bits/specfun.h:43,
from /usr/include/c++/13/cmath:3716,
from /usr/include/c++/13/math.h:36,
from aligner_seed2.h:97:
/usr/include/c++/13/bits/stl_pair.h:187:12: note: 'struct std::pair<DescentRedundancyKey, long int>' declared here
187 | struct pair
| ^~~~
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopyExact' at ds.h:965:7,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'push_back' at ds.h:496:29,
inlined from 'setupPatternComposer.constprop' at pat.cpp:309:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'setupPatternComposer.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopyExact' at ds.h:965:7,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'push_back' at ds.h:496:29,
inlined from 'setupPatternComposer.constprop' at pat.cpp:346:20:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'setupPatternComposer.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopyExact' at ds.h:965:7,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'push_back' at ds.h:496:29,
inlined from 'setupPatternComposer.constprop' at pat.cpp:363:20:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'setupPatternComposer.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'expand' at ds.h:505:29,
inlined from 'parseFasta' at sequence_io.h:88:15:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'parseFasta':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'expand' at ds.h:505:29,
inlined from 'parseFasta' at sequence_io.h:89:14:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'parseFasta':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandNoCopyExact' at ds.h:1003:17,
inlined from 'expandNoCopy' at ds.h:992:20,
inlined from 'operator=' at ds.h:405:32,
inlined from 'operator=' at ds.h:394:15,
inlined from '__ct ' at ds.h:373:9,
inlined from '__ct_base ' at pat.h:348:3:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In member function '__ct_base ':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function '__ct ',
inlined from 'driver.constprop' at bt2_search.cpp:4923:14:
outq.h:75:81: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
75 | perThreadBuf[i] = new BTString[perThreadBufSize_];
| ^
/usr/include/c++/13/new: In function 'driver.constprop':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'expand' at ds.h:505:29,
inlined from '__ct ' at pat.cpp:564:15,
inlined from 'patsrcFromStrings' at pat.cpp:100:57:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In function 'patsrcFromStrings':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from '_ZN5EListI11GroupWalk2SI10PListSliceImLi16384EELi16EELi128EE15expandCopyExactEm.part.0' at ds.h:967:17:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In member function '_ZN5EListI11GroupWalk2SI10PListSliceImLi16384EELi16EELi128EE15expandCopyExactEm.part.0':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
In member function 'alloc',
inlined from 'expandCopyExact' at ds.h:967:17,
inlined from 'expandCopyExact' at ds.h:965:7,
inlined from 'expandCopy' at ds.h:958:18,
inlined from 'expand' at ds.h:505:29,
inlined from 'instantiateSeeds.isra' at aligner_seed.cpp:434:15:
ds.h:923:26: warning: argument 1 value '18446744073709551615' exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
923 | T* tmp = new T[sz];
| ^
/usr/include/c++/13/new: In member function 'instantiateSeeds.isra':
/usr/include/c++/13/new:128:26: note: in a call to allocation function 'operator new []' declared here
128 | _GLIBCXX_NODISCARD void* operator new[](std::size_t) _GLIBCXX_THROW (std::bad_alloc)
| ^
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.bOtSmn
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le
++ dirname /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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,-D_FORTIFY_SOURCE=2 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bowtie2-2.4.1
+ /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le 'INSTALL=/usr/bin/install -p' PREFIX=/usr
mkdir -p /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin
for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \
cp -f $file /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin ; \
done
+ mkdir -p /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/man/man1
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ help2man -N -s 1 -o /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/man/man1/bowtie2.1 --version-string=2.4.1 /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin/bowtie2
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ help2man -N -s 1 -o /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/man/man1/bowtie2-build.1 --version-string=2.4.1 /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin/bowtie2-build
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ help2man -N -s 1 -o /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/man/man1/bowtie2-inspect.1 --version-string=2.4.1 /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin/bowtie2-inspect
+ /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 2.4.1-6.fc38 --unique-debug-suffix -2.4.1-6.fc38.ppc64le --unique-debug-src-base bowtie2-2.4.1-6.fc38.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/bowtie2-2.4.1
extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin/bowtie2-align-l
extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin/bowtie2-build-l
extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin/bowtie2-align-s
extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin/bowtie2-inspect-l
extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin/bowtie2-build-s
extracting debug info from /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/bin/bowtie2-inspect-s
original debug info size: 26176kB, size after compression: 18304kB
/usr/bin/sepdebugcrcfix: Updated 6 CRC32s, 0 CRC32s did match.
4935 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
+ /usr/lib/rpm/brp-remove-la-files
+ /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0
+ /usr/lib/rpm/redhat/brp-python-hardlink
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.0TjWAU
+ umask 022
+ cd /builddir/build/BUILD
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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,-D_FORTIFY_SOURCE=2 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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 -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -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
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes'
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd bowtie2-2.4.1
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ ./bowtie2 --version
+ grep 'version 2.4.1'
/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s version 2.4.1
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ ./bowtie2-build --version
+ grep 'version 2.4.1'
/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-build-s version 2.4.1
+ for cmd in bowtie2 bowtie2-{build,inspect}
+ ./bowtie2-inspect --version
+ grep 'version 2.4.1'
/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-inspect-s version 2.4.1
+ sed -i '/my $binary_type/ s/"release", "debug", "sanitized"/"release"/' scripts/test/simple_tests.pl
+ ASAN_OPTIONS=halt_on_error=1
+ UBSAN_OPTIONS=halt_on_error=1
+ scripts/test/simple_tests.pl --bowtie2=./bowtie2 --bowtie2-build=./bowtie2-build --compressed
\1 better written as $1 at scripts/test/simple_tests.pl line 4671.
\1 better written as $1 at scripts/test/simple_tests.pl line 4672.
FASTA-continuous 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 -F 10,9 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 6 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 6 -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 13 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --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
FASTA-continuous 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -F 10,9 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 12 -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 6 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 6 -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 12 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:12
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 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
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 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:1 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0 0 1 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Align should not fail when multiple seqs are all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
NNNNNNNNNNNNNNN
>2
AGCATCGATCAGTATCTGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:2 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0 0 2 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Should account for stretch of Ns at beginning (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:34
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Cline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG ABCDEDGHIJKLMNOP AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Cline 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO
Error: Read 0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Cline 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 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 --trim-to 5:12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 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 --trim-to 3:12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 11 -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 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU
trim-to: invalid position (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim-to 4:12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
--trim-to: trim position must be either 3 or 5
Bowtie 2 version 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]
<bt2-idx> Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<i> Files with interleaved paired-end FASTQ/FASTA reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<bam> Files are unaligned BAM sorted by read name.
<sam> File for SAM output (default: stdout)
<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
Options (defaults in parentheses):
Input:
-q query input files are FASTQ .fq/.fastq (default)
--tab5 query input files are TAB5 .tab5
--tab6 query input files are TAB6 .tab6
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
-r query input files are raw one-sequence-per-line
-F k:<int>,i:<int> query input files are continuous FASTA where reads
are substrings (k-mers) extracted from a FASTA file <s>
and aligned at offsets 1, 1+i, 1+2i ... end of reference
-c <m1>, <m2>, <r> are sequences themselves, not files
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
--trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
If the read end is not specified then it defaults to 3 (0)
--phred33 qualities are Phred+33 (default)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers
Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
Alignment:
-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)
-i <func> interval between seed substrings w/r/t read len (S,1,1.15)
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--dpad <int> include <int> extra ref chars on sides of DP table (15)
--gbar <int> disallow gaps within <int> nucs of read extremes (4)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)
--no-1mm-upfront do not allow 1 mismatch alignments before attempting to
scan for the optimal seeded alignments
--end-to-end entire read must align; no clipping (on)
OR
--local local alignment; ends might be soft clipped (off)
Scoring:
--ma <int> match bonus (0 for --end-to-end, 2 for --local)
--mp <int> max penalty for mismatch; lower qual = lower penalty (6)
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(G,20,8 for local, L,-0.6,-0.6 for end-to-end)
Reporting:
(default) look for multiple alignments, report best, with MAPQ
OR
-k <int> report up to <int> alns per read; MAPQ not meaningful
OR
-a/--all report all alignments; very slow, MAPQ not meaningful
Effort:
-D <int> give up extending after <int> failed extends in a row (15)
-R <int> for reads w/ repetitive seeds, try <int> sets of seeds (2)
Paired-end:
-I/--minins <int> minimum fragment length (0)
-X/--maxins <int> maximum fragment length (500)
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads
--dovetail concordant when mates extend past each other
--no-contain not concordant when one mate alignment contains other
--no-overlap not concordant when mates overlap at all
BAM:
--align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.
Use this option to align paired-end reads instead.
--preserve-tags Preserve tags from the original BAM record by
appending them to the end of the corresponding SAM output.
Output:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align to <path>
--al <path> write unpaired reads that aligned at least once to <path>
--un-conc <path> write pairs that didn't align concordantly to <path>
--al-conc <path> write pairs that aligned concordantly at least once to <path>
(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-unal suppress SAM records for unaligned reads
--no-head suppress header lines, i.e. lines starting with @
--no-sq suppress @SQ header lines
--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
--rg <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
--sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace
at the expense of generating non-standard SAM.
--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN
Performance:
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'bowtie's can share
Other:
--qc-filter filter out reads that are bad according to QSEQ filter
--seed <int> seed for random number generator (0)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
--version print version information and quit
-h/--help print this usage message
trim-to: invalid count (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim-to 5:-12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
Error: Encountered internal Bowtie 2 exception (#1)
Command: /builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
(ERR): bowtie2-align exited with value 1
--trim-to: the number bases to trim must be at least 0
Bowtie 2 version 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]
<bt2-idx> Index filename prefix (minus trailing .X.bt2).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<i> Files with interleaved paired-end FASTQ/FASTA reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<bam> Files are unaligned BAM sorted by read name.
<sam> File for SAM output (default: stdout)
<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
Options (defaults in parentheses):
Input:
-q query input files are FASTQ .fq/.fastq (default)
--tab5 query input files are TAB5 .tab5
--tab6 query input files are TAB6 .tab6
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
-r query input files are raw one-sequence-per-line
-F k:<int>,i:<int> query input files are continuous FASTA where reads
are substrings (k-mers) extracted from a FASTA file <s>
and aligned at offsets 1, 1+i, 1+2i ... end of reference
-c <m1>, <m2>, <r> are sequences themselves, not files
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
--trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
If the read end is not specified then it defaults to 3 (0)
--phred33 qualities are Phred+33 (default)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers
Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
Alignment:
-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)
-i <func> interval between seed substrings w/r/t read len (S,1,1.15)
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--dpad <int> include <int> extra ref chars on sides of DP table (15)
--gbar <int> disallow gaps within <int> nucs of read extremes (4)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)
--no-1mm-upfront do not allow 1 mismatch alignments before attempting to
scan for the optimal seeded alignments
--end-to-end entire read must align; no clipping (on)
OR
--local local alignment; ends might be soft clipped (off)
Scoring:
--ma <int> match bonus (0 for --end-to-end, 2 for --local)
--mp <int> max penalty for mismatch; lower qual = lower penalty (6)
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(G,20,8 for local, L,-0.6,-0.6 for end-to-end)
Reporting:
(default) look for multiple alignments, report best, with MAPQ
OR
-k <int> report up to <int> alns per read; MAPQ not meaningful
OR
-a/--all report all alignments; very slow, MAPQ not meaningful
Effort:
-D <int> give up extending after <int> failed extends in a row (15)
-R <int> for reads w/ repetitive seeds, try <int> sets of seeds (2)
Paired-end:
-I/--minins <int> minimum fragment length (0)
-X/--maxins <int> maximum fragment length (500)
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads
--dovetail concordant when mates extend past each other
--no-contain not concordant when one mate alignment contains other
--no-overlap not concordant when mates overlap at all
BAM:
--align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.
Use this option to align paired-end reads instead.
--preserve-tags Preserve tags from the original BAM record by
appending them to the end of the corresponding SAM output.
Output:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align to <path>
--al <path> write unpaired reads that aligned at least once to <path>
--un-conc <path> write pairs that didn't align concordantly to <path>
--al-conc <path> write pairs that aligned concordantly at least once to <path>
(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-unal suppress SAM records for unaligned reads
--no-head suppress header lines, i.e. lines starting with @
--no-sq suppress @SQ header lines
--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
--rg <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
--sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace
at the expense of generating non-standard SAM.
--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN
Performance:
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'bowtie's can share
Other:
--qc-filter filter out reads that are bad according to QSEQ filter
--seed <int> seed for random number generator (0)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
--version print version information and quit
-h/--help print this usage message
Cline 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
Error: Encountered internal Bowtie 2 exception (#1)
Command: /builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
(ERR): bowtie2-align exited with value 1
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU
Cline 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
Cline multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -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 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Cline multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII"
0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Cline paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII"
1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Cline paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 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 -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 3 -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 14 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Fastq 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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -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 3 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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
Fastq 4 (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 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fastq 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 5 -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 7 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -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 3 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 3 -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 7 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -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 6 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Fastq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Fastq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
Fastq paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP
r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN
Fasta 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 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 8 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Fasta 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fasta 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --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 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -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 11 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN
Fasta 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -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 14 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Fasta multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Fasta multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Fasta multiline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --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
r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Fasta multiline 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Fasta multiline 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
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 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP
Fasta paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP
Fasta paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -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 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -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 4 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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 3 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Raw 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -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 15 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 15 -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 16 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -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 13 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 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 multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 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
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 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
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 1 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -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 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
Raw paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -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 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Tabbed 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Tabbed 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --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 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Tabbed 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
Error: Read r0 has more quality values than read characters.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Tabbed 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim3 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 8 -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 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 6 -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 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -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 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
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 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Tabbed multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Tabbed paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Tabbed paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -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 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
Tabbed paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP
r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN
Qseq 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 5049.
Qseq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --quiet -a --reads-per-batch 1 -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 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -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 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Qseq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Qseq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Qseq paired 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index 99 0 1 255 10M = 9 19 AGCATCGATC ABCBGACBCB AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
MachName_RunNum_Lane_Tile_10_10_Index 147 0 9 255 11M = 1 -19 TCAAAAACTGA ABCBCAGBCBA AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Qseq paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:73
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 3 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:73
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:73
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 5 24 20M1D45M * 0 0 TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20^A0A44 YT:Z:UU
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1192
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 3 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1028
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 65 0 3 42 38M = 982 1021 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:DP
r0 129 0 982 42 42M = 3 -1021 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:DP
MREVERSE flag is set if mate does not align (fw:1, sam:1)
References:
>0
TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --fr --quiet --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:250
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 16 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:290
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 13 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:54
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:54
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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^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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:54
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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^A0A39 YT:Z:UU
MD:Z 2 (fw:0, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:54
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU
MD:Z 3 (fw:1, sam:1)
References:
>0
CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:55
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:55
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:55
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:55
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-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:1.0 SO:unsorted
@SQ SN:0 LN:4
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:4
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 1 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:4
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;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 0 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU
Local alignment 2 (fw:0, sam:1)
References:
>0
TTGA
./bowtie2 --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:4
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU
Local alignment 3 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 6 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:86
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 16 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:86
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 15 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:86
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 1 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:86
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 1 -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 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
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:407
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 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 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r2 99 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP
r2 147 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP
Mate reporting order, -a (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:407
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 339 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 419 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 339 0 169 255 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 419 0 104 255 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 419 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 339 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 419 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 339 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 419 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 99 0 104 1 19M = 169 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 147 0 169 1 19M = 104 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 355 0 3 255 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 403 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 403 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 355 0 104 255 19M = 270 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 403 0 270 255 19M = 104 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 355 0 205 255 19M = 270 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 403 0 270 255 19M = 205 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 355 0 3 255 19M = 270 286 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r1 403 0 270 255 19M = 3 -286 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r2 83 0 379 255 26M = 307 -98 AAAACGCTCTAGTCAGCTCATTGGCT IIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:26 YS:i:0 YT:Z:CP
r2 163 0 307 255 30M = 379 98 ATACGGCCATCGCGGCGGCATTACTCGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YS:i:0 YT:Z:CP
Mate reporting order, -M 1 (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA
./bowtie2 --fr --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:407
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0 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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:407
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz"
r0 83 0 169 1 19M = 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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
Non-overlapping; --no-discordant (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --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-discordant (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --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; --no-discordant --no-mixed (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 9 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 2 42 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP
r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP
Overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP
r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP
Overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-dovetail --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 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-contain --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 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-contain --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-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --no-overlap --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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:105
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:105
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --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:-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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 --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:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU
Scoring params 4 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --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:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 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 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --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:-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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --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 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -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:-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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU
Q XS:i 1a (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 8M * 0 0 TTGTTCGT 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 8M * 0 0 TTGTTCGT 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 8M * 0 0 TTGTTCGT 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:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-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:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU
Q XS:i 1b --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --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:-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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --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 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:68
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:68
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:528
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 8 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:528
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 12 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
XS:i 1 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU
XS:i 1 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 4 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 10 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --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 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
XS:i 4a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:24
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:24
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 11 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:24
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 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 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:24
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
XS:i 5a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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:1.0 SO:unsorted
@SQ SN:0 LN:120
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
XS:i 5b (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 6 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 10 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU
BWA-SW-like 2 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU
BWA-SW-like 2 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU
BWA-SW-like 3 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --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:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU
BWA-SW-like 3 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 2 -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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 99 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP
r0 147 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP
SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP
r0 131 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP
SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --rf --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 4 255 24M = 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 4 255 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 12 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 4 255 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@SQ SN:1 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU
matchesRef regression 4 (fw:0, sam:1)
References:
>0
CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC
>1
GCTCGGAATTCGTGCTCCGNCCCGTACGGTT
./bowtie2 --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@SQ SN:1 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU
matchesRef regression 3 (fw:1, sam:1)
References:
>0
GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 15 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 9 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@SQ SN:1 LN:27
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 8 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@SQ SN:1 LN:27
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 4 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:61
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 10 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:61
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 10 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:23
@SQ SN:1 LN:28
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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 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 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:1.0 SO:unsorted
@SQ SN:0 LN:23
@SQ SN:1 LN:28
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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"
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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 11 -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 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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 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"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -s 2 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 10 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 5 -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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 6 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:3
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 4 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:3
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 4 -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:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 8 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --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 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 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 --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:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -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 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:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 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 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU
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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP
r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP
P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP
r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP
P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT
./bowtie2 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 8 -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:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 9 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 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: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:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 1 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 316 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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 1 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP
r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP
P.k.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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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.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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP
r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP
r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP
r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP
P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP
r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP
r0 147 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP
P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP
r0 163 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP
P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 -X 150 --local --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 4 -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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 10 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:2607
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 8 -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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:2607
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1906
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP
r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP
P.M.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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1906
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 2 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 13 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 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.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --local --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, 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:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 10 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 15 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --quiet -M 2 --local --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 2 -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:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 6 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --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:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --local --quiet -k 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 -X 150 --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 13 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 3 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 12 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 1 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 5 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 9 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 12 -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:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:49
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:49
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy 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 12 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy 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 12 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 6 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU
Gap penalties 4 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy 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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 11 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 11 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:18
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:18
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 TTGTTGTTTGATTCGT IIIIIIIIIIIIIIII YT:Z:UU
Gap penalties 7 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU
N filtering 1 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 12 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU
N filtering 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 3 (fw:0, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 9 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU
N filtering 4 (fw:0, sam:1)
References:
>0
GAGACTTTNTACGCATCGAACTATCGCTCTA
./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 1 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 4 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 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 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU
(fw:1, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:13
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU
(fw:0, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:13
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:13
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTT
./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:13
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:5
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:5
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:5
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:5
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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:1.0 SO:unsorted
@SQ SN:0 LN:25
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:25
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:37
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
(fw: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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:37
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:37
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
(fw:0, sam:1)
References:
>0
ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN
./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:37
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 272 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
(fw: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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 11 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:10
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 13 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:10
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 5 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:22
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:22
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 10 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz"
r0 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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 14 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP
r0 129 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP
r1 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r1 131 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Simple paired-end 12 (fw:0, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC
./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0 113 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP
r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP
r1 115 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r1 179 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Simple paired-end 11 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 15 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:41
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --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 -I 28 -X 80 --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:1.0 SO:unsorted
@SQ SN:0 LN:41
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 11 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:81
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 147 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Simple paired-end 9 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:81
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 163 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Simple paired-end 8 (fw:1, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:81
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 147 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 355 0 4 255 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 403 0 60 255 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 355 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 403 0 60 255 10M = 38 -32 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Simple paired-end 8 (fw:0, sam:1)
References:
>0
CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC
./bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:81
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 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 --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 12 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 14 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 12 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:49
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 0 0 44 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 0 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 0 0 42 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:49
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 16 0 26 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 16 0 17 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 16 0 40 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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"
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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --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 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --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 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 13 -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:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 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 15 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 15 -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 15 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 15 -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 7 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz"
seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU
FASTA-continuous 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz"
seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU
FASTA-continuous 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz"
seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU
FASTA-continuous 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAG
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index -F 10,1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:12
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz"
seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU
seq1_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 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:1 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0 0 1 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Align should not fail when multiple seqs are all Ns (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNN
>1
NNNNNNNNNNNNNNN
>2
AGCATCGATCAGTATCTGA
./bowtie2-build --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 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:2 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0 0 2 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Should account for stretch of Ns at beginning (fw:1, sam:1)
References:
>0
NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:34
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG"
0 0 0 18 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Cline 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -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 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 4 -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 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 8 -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 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 12 -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 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 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: invalid position (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --trim-to 4:12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
--trim-to: trim position must be either 3 or 5
Bowtie 2 version 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]
<bt2-idx> Index filename prefix (minus trailing .X.bt2l).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<i> Files with interleaved paired-end FASTQ/FASTA reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<bam> Files are unaligned BAM sorted by read name.
<sam> File for SAM output (default: stdout)
<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
Options (defaults in parentheses):
Input:
-q query input files are FASTQ .fq/.fastq (default)
--tab5 query input files are TAB5 .tab5
--tab6 query input files are TAB6 .tab6
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
-r query input files are raw one-sequence-per-line
-F k:<int>,i:<int> query input files are continuous FASTA where reads
are substrings (k-mers) extracted from a FASTA file <s>
and aligned at offsets 1, 1+i, 1+2i ... end of reference
-c <m1>, <m2>, <r> are sequences themselves, not files
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
--trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
If the read end is not specified then it defaults to 3 (0)
--phred33 qualities are Phred+33 (default)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers
Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
Alignment:
-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)
-i <func> interval between seed substrings w/r/t read len (S,1,1.15)
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--dpad <int> include <int> extra ref chars on sides of DP table (15)
--gbar <int> disallow gaps within <int> nucs of read extremes (4)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)
--no-1mm-upfront do not allow 1 mismatch alignments before attempting to
scan for the optimal seeded alignments
--end-to-end entire read must align; no clipping (on)
OR
--local local alignment; ends might be soft clipped (off)
Scoring:
--ma <int> match bonus (0 for --end-to-end, 2 for --local)
--mp <int> max penalty for mismatch; lower qual = lower penalty (6)
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(G,20,8 for local, L,-0.6,-0.6 for end-to-end)
Reporting:
(default) look for multiple alignments, report best, with MAPQ
OR
-k <int> report up to <int> alns per read; MAPQ not meaningful
OR
-a/--all report all alignments; very slow, MAPQ not meaningful
Effort:
-D <int> give up extending after <int> failed extends in a row (15)
-R <int> for reads w/ repetitive seeds, try <int> sets of seeds (2)
Paired-end:
-I/--minins <int> minimum fragment length (0)
-X/--maxins <int> maximum fragment length (500)
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads
--dovetail concordant when mates extend past each other
--no-contain not concordant when one mate alignment contains other
--no-overlap not concordant when mates overlap at all
BAM:
--align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.
Use this option to align paired-end reads instead.
--preserve-tags Preserve tags from the original BAM record by
appending them to the end of the corresponding SAM output.
Output:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align to <path>
--al <path> write unpaired reads that aligned at least once to <path>
--un-conc <path> write pairs that didn't align concordantly to <path>
--al-conc <path> write pairs that aligned concordantly at least once to <path>
(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-unal suppress SAM records for unaligned reads
--no-head suppress header lines, i.e. lines starting with @
--no-sq suppress @SQ header lines
--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
--rg <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
--sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace
at the expense of generating non-standard SAM.
--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN
Performance:
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'bowtie's can share
Other:
--qc-filter filter out reads that are bad according to QSEQ filter
--seed <int> seed for random number generator (0)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
--version print version information and quit
-h/--help print this usage message
trim-to: invalid count (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
Error: Encountered internal Bowtie 2 exception (#1)
Command: /builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
(ERR): bowtie2-align exited with value 1
--trim-to: the number bases to trim must be at least 0
Bowtie 2 version 2.4.1 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea)
Usage:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r> | --interleaved <i> | -b <bam>} [-S <sam>]
<bt2-idx> Index filename prefix (minus trailing .X.bt2l).
NOTE: Bowtie 1 and Bowtie 2 indexes are not compatible.
<m1> Files with #1 mates, paired with files in <m2>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<m2> Files with #2 mates, paired with files in <m1>.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<r> Files with unpaired reads.
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<i> Files with interleaved paired-end FASTQ/FASTA reads
Could be gzip'ed (extension: .gz) or bzip2'ed (extension: .bz2).
<bam> Files are unaligned BAM sorted by read name.
<sam> File for SAM output (default: stdout)
<m1>, <m2>, <r> can be comma-separated lists (no whitespace) and can be
specified many times. E.g. '-U file1.fq,file2.fq -U file3.fq'.
Options (defaults in parentheses):
Input:
-q query input files are FASTQ .fq/.fastq (default)
--tab5 query input files are TAB5 .tab5
--tab6 query input files are TAB6 .tab6
--qseq query input files are in Illumina's qseq format
-f query input files are (multi-)FASTA .fa/.mfa
-r query input files are raw one-sequence-per-line
-F k:<int>,i:<int> query input files are continuous FASTA where reads
are substrings (k-mers) extracted from a FASTA file <s>
and aligned at offsets 1, 1+i, 1+2i ... end of reference
-c <m1>, <m2>, <r> are sequences themselves, not files
-s/--skip <int> skip the first <int> reads/pairs in the input (none)
-u/--upto <int> stop after first <int> reads/pairs (no limit)
-5/--trim5 <int> trim <int> bases from 5'/left end of reads (0)
-3/--trim3 <int> trim <int> bases from 3'/right end of reads (0)
--trim-to [3:|5:]<int> trim reads exceeding <int> bases from either 3' or 5' end
If the read end is not specified then it defaults to 3 (0)
--phred33 qualities are Phred+33 (default)
--phred64 qualities are Phred+64
--int-quals qualities encoded as space-delimited integers
Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50
Alignment:
-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)
-i <func> interval between seed substrings w/r/t read len (S,1,1.15)
--n-ceil <func> func for max # non-A/C/G/Ts permitted in aln (L,0,0.15)
--dpad <int> include <int> extra ref chars on sides of DP table (15)
--gbar <int> disallow gaps within <int> nucs of read extremes (4)
--ignore-quals treat all quality values as 30 on Phred scale (off)
--nofw do not align forward (original) version of read (off)
--norc do not align reverse-complement version of read (off)
--no-1mm-upfront do not allow 1 mismatch alignments before attempting to
scan for the optimal seeded alignments
--end-to-end entire read must align; no clipping (on)
OR
--local local alignment; ends might be soft clipped (off)
Scoring:
--ma <int> match bonus (0 for --end-to-end, 2 for --local)
--mp <int> max penalty for mismatch; lower qual = lower penalty (6)
--np <int> penalty for non-A/C/G/Ts in read/ref (1)
--rdg <int>,<int> read gap open, extend penalties (5,3)
--rfg <int>,<int> reference gap open, extend penalties (5,3)
--score-min <func> min acceptable alignment score w/r/t read length
(G,20,8 for local, L,-0.6,-0.6 for end-to-end)
Reporting:
(default) look for multiple alignments, report best, with MAPQ
OR
-k <int> report up to <int> alns per read; MAPQ not meaningful
OR
-a/--all report all alignments; very slow, MAPQ not meaningful
Effort:
-D <int> give up extending after <int> failed extends in a row (15)
-R <int> for reads w/ repetitive seeds, try <int> sets of seeds (2)
Paired-end:
-I/--minins <int> minimum fragment length (0)
-X/--maxins <int> maximum fragment length (500)
--fr/--rf/--ff -1, -2 mates align fw/rev, rev/fw, fw/fw (--fr)
--no-mixed suppress unpaired alignments for paired reads
--no-discordant suppress discordant alignments for paired reads
--dovetail concordant when mates extend past each other
--no-contain not concordant when one mate alignment contains other
--no-overlap not concordant when mates overlap at all
BAM:
--align-paired-reads Bowtie2 will, by default, attempt to align unpaired BAM reads.
Use this option to align paired-end reads instead.
--preserve-tags Preserve tags from the original BAM record by
appending them to the end of the corresponding SAM output.
Output:
-t/--time print wall-clock time taken by search phases
--un <path> write unpaired reads that didn't align to <path>
--al <path> write unpaired reads that aligned at least once to <path>
--un-conc <path> write pairs that didn't align concordantly to <path>
--al-conc <path> write pairs that aligned concordantly at least once to <path>
(Note: for --un, --al, --un-conc, or --al-conc, add '-gz' to the option name, e.g.
--un-gz <path>, to gzip compress output, or add '-bz2' to bzip2 compress output.)
--quiet print nothing to stderr except serious errors
--met-file <path> send metrics to file at <path> (off)
--met-stderr send metrics to stderr (off)
--met <int> report internal counters & metrics every <int> secs (1)
--no-unal suppress SAM records for unaligned reads
--no-head suppress header lines, i.e. lines starting with @
--no-sq suppress @SQ header lines
--rg-id <text> set read group id, reflected in @RG line and RG:Z: opt field
--rg <text> add <text> ("lab:value") to @RG line of SAM header.
Note: @RG line only printed when --rg-id is set.
--omit-sec-seq put '*' in SEQ and QUAL fields for secondary alignments.
--sam-no-qname-trunc Suppress standard behavior of truncating readname at first whitespace
at the expense of generating non-standard SAM.
--xeq Use '='/'X', instead of 'M,' to specify matches/mismatches in SAM record.
--soft-clipped-unmapped-tlen Exclude soft-clipped bases when reporting TLEN
Performance:
-p/--threads <int> number of alignment threads to launch (1)
--reorder force SAM output order to match order of input reads
--mm use memory-mapped I/O for index; many 'bowtie's can share
Other:
--qc-filter filter out reads that are bad according to QSEQ filter
--seed <int> seed for random number generator (0)
--non-deterministic seed rand. gen. arbitrarily instead of using read attributes
--version print version information and quit
-h/--help print this usage message
Cline 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
Error: Encountered internal Bowtie 2 exception (#1)
Command: /builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
(ERR): bowtie2-align exited with value 1
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII"
0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU
Cline 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 5 -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 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -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 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Cline multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Cline multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 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 --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 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 --large-index -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -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 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -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 10 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 10 -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 6 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 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
Fastq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -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 16 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -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 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 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz
Error: Read r0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fastq 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 15 -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 14 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 14 -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 7 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 --large-index -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -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 8 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 8 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -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 2 -x .simple_tests.tmp -q .simple_tests.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --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
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 9 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -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 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz"
r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
Fastq paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 1 -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 7 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 15M * 0 0 CATCGATCAGTATCT IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Fasta 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 7 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Fasta 5 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fasta 6 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz
Error: reads file does not look like a FASTA file
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Fasta 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 8 -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 8 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN
Fasta 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz"
Fasta multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 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 11 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Fasta multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -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 13 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Fasta multiline 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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 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 15 -x .simple_tests.tmp -f .simple_tests.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
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 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz"
r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP
Fasta paired 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --large-index -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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -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 14 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 14 -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 1 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Raw 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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -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 9 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Raw 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -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 15 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 15 -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 11 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz"
Raw multiread 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz"
0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Raw multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 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 multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -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 --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 -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Raw paired 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP
Raw paired 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAAAAACTGA
./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz"
0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP
0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN
Tabbed 1 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Tabbed 2 (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
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --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 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Tabbed 4 (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 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 12 -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 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -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 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 2 -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 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -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 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
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 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
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 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz"
r0 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 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -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 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --large-index -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 3 -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 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 4 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values.
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)
Qseq 7 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 8 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN
Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5049.
Qseq 9 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -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 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU
Qseq multiread 2 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz"
MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
Qseq multiread 3 (fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 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
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 16 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -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 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 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 --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:73
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 3 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:73
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 16 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:73
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 15 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1192
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 5 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1028
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 65 0 3 42 38M = 982 1021 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:DP
r0 129 0 982 42 42M = 3 -1021 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:DP
MREVERSE flag is set if mate does not align (fw:1, sam:1)
References:
>0
TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:250
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 89 0 51 42 100M = 51 0 TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UP
r0 165 0 51 0 * = 51 0 CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP
Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1)
References:
>0
CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:290
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 3 1 38M = 246 285 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:CP
r0 147 0 246 1 42M = 3 -285 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:CP
MD:Z 1 (fw:1, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:54
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU
MD:Z 1 (fw:0, sam:1)
References:
>0
CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:54
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU
MD:Z 2 (fw:1, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2-build --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:1.0 SO:unsorted
@SQ SN:0 LN:54
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 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^A0A39 YT:Z:UU
MD:Z 2 (fw:0, sam:1)
References:
>0
CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA
./bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:54
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:55
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:55
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:55
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:55
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU
Local alignment 1 (fw:1, sam:1)
References:
>0
TTGT
./bowtie2-build --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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:4
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 4 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:4
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 4 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:4
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 14 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:4
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 15 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 12 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 12 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:86
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU
r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU
r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU
Alignment order -k (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:86
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU
r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU
r0 272 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU
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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:86
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU
r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU
r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU
r0 256 0 71 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-22 XS:i:-6 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G0T0G0T5 YT:Z:UU
Alignment order -a (fw:0, sam:1)
References:
>0
GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA
./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:86
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:407
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -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 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:1.0 SO:unsorted
@SQ SN:0 LN:407
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 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 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 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
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:407
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 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 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:407
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 15 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
Non-overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
Non-overlapping; --no-discordant (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --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-discordant (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --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 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
Non-overlapping; --no-dovetail (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
Non-overlapping; --no-dovetail (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
Non-overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
Non-overlapping; --no-overlap (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP
r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP
Overlapping; no args (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP
r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP
Overlapping; no args (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 4 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-dovetail --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 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP
r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP
Overlapping; --no-contain (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP
r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP
Overlapping; --no-contain (fw:0, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP
r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP
Overlapping; --no-overlap (fw:1, sam:1)
References:
>0
AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA
./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --no-overlap --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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:105
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:105
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --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:-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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 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:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU
Scoring params 4 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU
Scoring params 4 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU
Scoring params 6 (fw:1, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU
Scoring params 6 (fw:0, sam:1)
References:
>0
ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG
./bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:102
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU
Q XS:i 1a ! --mp 3,6 (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 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 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -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 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU
Q XS:i 1a I --mp 3,6 (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU
Q XS:i 1a --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 9 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 0 8M * 0 0 TTGTTCGT 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:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU
Q XS:i 1c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU
Q XS:i 1c --ignore-quals (fw:1, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU
Q XS:i 1c --ignore-quals (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGA
./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 0 8M * 0 0 TTGTTCGT 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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:68
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:68
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 6 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:528
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 6 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:528
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 2 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --large-index --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --large-index --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --large-index --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --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 3c (fw:0, sam:1)
References:
>0
TTGTTCGATTGTTCGT
./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
XS:i 4a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGT
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:24
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:24
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
XS:i 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:24
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 11 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:24
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
XS:i 5a (fw:1, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
XS:i 5a (fw:0, sam:1)
References:
>0
TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA
./bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU
BWA-SW-like 1 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU
BWA-SW-like 1 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 12 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU
BWA-SW-like 3 (fw:1, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU
BWA-SW-like 3 (fw:0, sam:1)
References:
>0
GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA
./bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:64
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU
SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP
r0 131 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP
SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --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:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP
r0 163 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP
SAM paired-end where both mates align 3 (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --large-index --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:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP
r0 131 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP
SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --large-index --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 73 0 4 255 24M = 4 0 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YT:Z:UP
r0 133 0 4 0 * = 4 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP
SAM paired-end where neither mate aligns (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --large-index --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP
r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP
SAM paired-end where both mates align, but discordantly (fw:1, sam:1)
References:
>0
GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC
./bowtie2 --large-index --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:69
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@SQ SN:1 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 15 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:120
@SQ SN:1 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 12 -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:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 11 -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:1.0 SO:unsorted
@SQ SN:0 LN:47
@SQ SN:1 LN:27
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:47
@SQ SN:1 LN:27
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 5 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:61
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:61
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 10 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:23
@SQ SN:1 LN:28
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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 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 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:1.0 SO:unsorted
@SQ SN:0 LN:23
@SQ SN:1 LN:28
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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"
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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1 0 0 4 255 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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 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 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:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 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"
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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 2 -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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:0, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
(fw:1, sam:1)
References:
>0
AGCATCGATCAGTATCTGA
./bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 16 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 11 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 6 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 6 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:19
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r1 0 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU
(fw:1, sam:1)
References:
>0
TGC
./bowtie2-build --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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:3
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:3
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 1 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -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:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU
r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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,.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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz"
r0 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:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGT
./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 15 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 8 -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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 4 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 8 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 961 1 28M = 13 -976 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1000
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 1000 --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 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:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 2 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 4 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 14 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 15 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 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: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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 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:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:363
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP
r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP
P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA
./bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP
r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP
P.k.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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 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: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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 3 -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:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 3 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:126
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 9 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:2607
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 6 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:2607
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 8 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1906
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 99 0 1672 1 33M = 1738 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP
r0 147 0 1738 1 28M = 1672 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP
P.M.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC
./bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:1906
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 83 0 1738 1 28M = 1672 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP
r0 163 0 1672 1 33M = 1738 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP
U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU
U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --large-index --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU
U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 4 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 8 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU
U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1)
References:
>0
AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA
./bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 9 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:56
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 6 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --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: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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 8 -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:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --large-index --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, 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:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --large-index --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --large-index --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 10 -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:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 11 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 --large-index --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 16 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 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: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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:85
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 134 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 134 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1)
References:
>0
AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA
./bowtie2 --large-index --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 12 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 3 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 5 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:340
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 262 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
r0 272 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
r0 272 0 304 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
r0 272 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU
r0 256 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:49
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 0 0 35 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 0 0 5 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 0 0 31 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
(fw:0, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:49
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r2 16 0 39 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r3 16 0 1 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r4 16 0 43 255 2M * 0 0 CC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
Gap penalties 1 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 10 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 10 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy 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 16 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU
Gap penalties 4 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 10 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:18
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 0 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU
Gap penalties 6 (fw:0, sam:1)
References:
>0
ATTGTTCGTTTGTTCGTA
./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:18
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU
Gap penalties 7 (fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 TTGTTGTTTGATTCGT IIIIIIIIIIIIIIII YT:Z:UU
Gap penalties 7 (fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU
N filtering 1 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAACTATCGCTCTA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 6 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU
N filtering 2 (fw:0, sam:1)
References:
>0
GAGACTTTATNCGCATCGAACTATCGCTCTA
./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU
N filtering 3 (fw:1, sam:1)
References:
>0
GAGACTTTATACGCATCGAANTATCGCTCTA
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 12 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 2 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:31
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU
(fw:1, sam:1)
References:
>0
TTTTGTTCGTTTG
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:13
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:13
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:13
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:13
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 255 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:5
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:5
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:5
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:5
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:25
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:25
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:37
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 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: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:1.0 SO:unsorted
@SQ SN:0 LN:37
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:37
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU
(fw: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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:37
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 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: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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz"
r0 0 0 1 255 8M * 0 0 TTGTTGGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU
r1 0 0 1 255 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU
(fw:1, sam:1)
References:
>0
ATAACCTTCG
./bowtie2-build --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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:10
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 5 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:10
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:22
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -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:1.0 SO:unsorted
@SQ SN:0 LN:22
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 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 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:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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 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:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz"
r0 65 0 4 255 10M = 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 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 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 6 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:51
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 113 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP
r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP
Simple paired-end 10 (fw:1, sam:1)
References:
>0
TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:41
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 14 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:41
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 6 -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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:81
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:81
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 13 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:81
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 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
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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:81
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 8 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --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 --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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 10 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 8 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 67 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 131 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
Simple paired-end 1 (fw:0, sam:1)
References:
>0
CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC
./bowtie2 --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:53
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz"
r0 115 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
r0 179 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP
(fw:1, sam:1)
References:
>0
AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC
./bowtie2-build --large-index --quiet --sanity .simple_tests.pl.fa .simple_tests.tmp
./bowtie2 --large-index --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:49
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1 0 0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:49
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz"
r1 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:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
Warning: -M is deprecated. Use -D and -R to adjust effort instead.
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-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"
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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:8
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --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 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU
(fw:0, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 3 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU
(fw:1, sam:1)
References:
>0
TTGTTCGTTTGTTCGT
./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=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:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 4 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz
@HD VN:1.0 SO:unsorted
@SQ SN:0 LN:16
@PG ID:bowtie2 PN:bowtie2 VN:2.4.1 CL:"/builddir/build/BUILD/bowtie2-2.4.1/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz"
r0 16 0 1 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU
r0 272 0 9 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU
r0 272 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU
r0 272 0 6 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:0C0G0T2G0T1 YT:Z:UU
r0 272 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU
r0 272 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU
PASSED
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: bowtie2-2.4.1-6.fc38.ppc64le
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.TTiSzc
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie2-2.4.1
+ DOCDIR=/builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/doc/bowtie2
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/doc/bowtie2
+ cp -pr AUTHORS /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/doc/bowtie2
+ cp -pr MANUAL /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/doc/bowtie2
+ cp -pr MANUAL.markdown /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/doc/bowtie2
+ cp -pr NEWS /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/doc/bowtie2
+ cp -pr TUTORIAL /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/doc/bowtie2
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.nCQQOi
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie2-2.4.1
+ LICENSEDIR=/builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/licenses/bowtie2
+ export LC_ALL=C
+ LC_ALL=C
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/licenses/bowtie2
+ cp -pr LICENSE /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le/usr/share/licenses/bowtie2
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: bowtie2 = 2.4.1-6.fc38 bowtie2(ppc-64) = 2.4.1-6.fc38 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) 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_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(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-2.4.1-6.fc38.ppc64le
Provides: bowtie2-debugsource = 2.4.1-6.fc38 bowtie2-debugsource(ppc-64) = 2.4.1-6.fc38
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: bowtie2-debuginfo-2.4.1-6.fc38.ppc64le
Provides: bowtie2-debuginfo = 2.4.1-6.fc38 bowtie2-debuginfo(ppc-64) = 2.4.1-6.fc38 debuginfo(build-id) = 13fa174d2a4c97cab6c08e11df95eab283c32259 debuginfo(build-id) = 399aa3ae9784653a0dbcc8eda5560351170a85ec debuginfo(build-id) = 6863cf09713cbd8207916d70f24b5f94c1d029bd debuginfo(build-id) = b19531d5db70667bb21db33531a07227bae18c3d debuginfo(build-id) = fcb13c4026cf6a0d2264ae4109ae397979e15dea debuginfo(build-id) = fdda5011f2c00b8ddb500553945cd29fe788e9a4
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: bowtie2-debugsource(ppc-64) = 2.4.1-6.fc38
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le
Wrote: /builddir/build/RPMS/bowtie2-debugsource-2.4.1-6.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/bowtie2-2.4.1-6.fc38.ppc64le.rpm
Wrote: /builddir/build/RPMS/bowtie2-debuginfo-2.4.1-6.fc38.ppc64le.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.KxLHP0
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie2-2.4.1
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/bowtie2-2.4.1-6.fc38.ppc64le
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.zWbE3S
+ umask 022
+ cd /builddir/build/BUILD
+ rm -rf bowtie2-2.4.1 bowtie2-2.4.1.gemspec
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild bowtie2-2.4.1-6.fc38.src.rpm
Finish: build phase for bowtie2-2.4.1-6.fc38.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-rawhide-ppc64le-1671784311.816071/root/var/log/dnf.rpm.log
/var/lib/mock/fedora-rawhide-ppc64le-1671784311.816071/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-rawhide-ppc64le-1671784311.816071/root/var/log/dnf.log
INFO: Done(/var/lib/copr-rpmbuild/results/bowtie2-2.4.1-6.fc38.src.rpm) Config(child) 4 minutes 7 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