Diff of the two buildlogs: -- --- b1/build.log 2024-12-16 01:47:59.193101299 +0000 +++ b2/build.log 2024-12-16 01:59:14.694393039 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 17 20:03:56 -12 2026 -I: pbuilder-time-stamp: 1768723436 +I: Current time: Sun Jan 18 22:11:01 +14 2026 +I: pbuilder-time-stamp: 1768723861 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -36,52 +36,84 @@ dpkg-source: info: applying use-source-date-epoch-in-Makefile.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/718729/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2124697/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jan 18 08:11 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/2124697/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2124697/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='e1bff6c40c974839ba3101019670de52' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='718729' - PS1='# ' - PS2='> ' + INVOCATION_ID=16564bc8a1c44e1987a55de9346d7df9 + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2124697 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.BGfjv7C1/pbuilderrc_rCyY --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BGfjv7C1/b1 --logfile b1/build.log bowtie2_2.5.4-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.BGfjv7C1/pbuilderrc_PBVS --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.BGfjv7C1/b2 --logfile b2/build.log bowtie2_2.5.4-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink01-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/718729/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/2124697/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -212,7 +244,7 @@ Get: 69 http://deb.debian.org/debian unstable/main arm64 pandoc-data all 3.1.11.1-3 [459 kB] Get: 70 http://deb.debian.org/debian unstable/main arm64 pandoc arm64 3.1.11.1+ds-2 [26.2 MB] Get: 71 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 55.4 MB in 0s (158 MB/s) +Fetched 55.4 MB in 0s (166 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package liblocale-gettext-perl. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20082 files and directories currently installed.) @@ -469,8 +501,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Jan 18 08:04:17 UTC 2026. -Universal Time is now: Sun Jan 18 08:04:17 UTC 2026. +Local time is now: Sun Jan 18 08:11:23 UTC 2026. +Universal Time is now: Sun Jan 18 08:11:23 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -527,7 +559,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/bowtie2-2.5.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bowtie2_2.5.4-1_source.changes +I: user script /srv/workspace/pbuilder/2124697/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2124697/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/bowtie2-2.5.4/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../bowtie2_2.5.4-1_source.changes dpkg-buildpackage: info: source package bowtie2 dpkg-buildpackage: info: source version 2.5.4-1 dpkg-buildpackage: info: source distribution unstable @@ -620,6 +656,8 @@ bt2_search.cpp:4626:20: note: call to ‘int closedir(DIR*)’ here 4626 | if(closedir(dir) != 0) { | ~~~~~~~~^~~~~ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ bt2_search.cpp: In function ‘int read_dir(const char*, int*)’: bt2_search.cpp:4628:67: warning: pointer ‘dir’ may be used after ‘int closedir(DIR*)’ [-Wuse-after-free] 4628 | cerr << "read_dir: could not close directory " << dir << endl; @@ -642,9 +680,6 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/c++/14/istream:41, from /usr/include/c++/14/fstream:40, from bt2_search.cpp:22: @@ -663,6 +698,7 @@ bt2_search.cpp:4626:20: note: call to ‘int closedir(DIR*)’ here 4626 | if(closedir(dir) != 0) { | ~~~~~~~~^~~~~ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from /usr/include/c++/14/istream:41, from /usr/include/c++/14/fstream:40, from bt2_search.cpp:22: @@ -765,29 +801,29 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, from aligner_sw.cpp:25: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, - from aligner_sw.cpp:25: + from aligner_sw_driver.h:81, + from aligner_sw_driver.cpp:47: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, - from aligner_sw_driver.h:81, - from aligner_sw_driver.cpp:47: + from aligner_sw.cpp:25: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, from aligner_sw_driver.h:81, from aligner_sw_driver.cpp:47: @@ -825,8 +861,6 @@ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, from aligner_swsse_loc_i16.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] @@ -835,41 +869,43 @@ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, - from aligner_swsse_loc_i16.cpp:56: + from aligner_swsse_ee_i16.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, - from aligner_swsse_ee_i16.cpp:56: + from aligner_swsse_loc_i16.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, - from aligner_swsse_ee_i16.cpp:56: + from aligner_swsse_loc_u8.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, - from aligner_swsse_loc_u8.cpp:56: + from aligner_swsse_ee_i16.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ -cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, from aligner_swsse_ee_u8.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ +cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ is not valid for C++ In file included from aligner_sw.h:75, from aligner_swsse_loc_u8.cpp:56: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] @@ -908,20 +944,20 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -F 10,9 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,9 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 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 16 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 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 @@ -929,38 +965,38 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -F 10,9 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,9 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -F 10,9 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,9 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz" seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz" seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 6 (fw:1, sam:1) References: >0 AGCATCGATCAG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -F 10,1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:12 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 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 @@ -973,11 +1009,11 @@ ./bowtie2-build --quiet .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 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:15 @SQ SN:1 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 0 0 1 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Align should not fail when multiple seqs are all Ns (fw:1, sam:1) References: @@ -992,60 +1028,59 @@ 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 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:15 @SQ SN:1 LN:15 @SQ SN:2 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 0 0 2 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Should account for stretch of Ns at beginning (fw:1, sam:1) References: >0 NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:34 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -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 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP +./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG ABCDEDGHIJKLMNOP AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO +./bowtie2 --quiet -a --reads-per-batch 16 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Cline 5 (fw:1, sam:1) References: >0 @@ -1053,43 +1088,42 @@ ./bowtie2 --quiet -a --reads-per-batch 10 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) trim-to: trim from 5'-end (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim-to 5:12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim-to 5:12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 7 255 12M * 0 0 GATCAGTATCTG IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: trim from 3'-end (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim-to 3:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim-to 3:12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: trim from 3'-end (default) (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim-to 12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim-to 12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: invalid position (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim-to 4:12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim-to 4:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: trim position must be either 3 or 5 Bowtie 2 version 2.5.4 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -1244,13 +1278,13 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 trim-to: invalid count (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim-to 5:-12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim-to 5:-12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: the number bases to trim must be at least 0 Bowtie 2 version 2.5.4 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -1405,26 +1439,26 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 Cline 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim3 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 8 -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 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim5 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 6 -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: @@ -1438,34 +1472,34 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -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 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG +./bowtie2 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 7 -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) @@ -1473,10 +1507,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII +./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 @@ -1485,30 +1519,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Cline paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Cline paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII +./bowtie2 -3 7 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN Fastq 1 (fw:1, sam:1) @@ -1516,109 +1550,106 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --quiet -a --reads-per-batch 7 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fastq 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fastq 6 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --quiet -a --reads-per-batch 1 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fastq 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Fastq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim5 16 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 14 -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 9 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -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 5 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 9 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq paired 1 (fw:1, sam:1) @@ -1626,10 +1657,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 @@ -1638,30 +1669,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Fastq paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 -3 7 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 8 -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) @@ -1669,55 +1700,53 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 9 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -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 2 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --quiet -a --reads-per-batch 6 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fasta 6 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --quiet -a --reads-per-batch 15 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fasta 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Fasta 8 (fw:1, sam:1) References: @@ -1732,67 +1761,67 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -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 +./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII 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 15 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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) @@ -1800,10 +1829,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP @@ -1812,30 +1841,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -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 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -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 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN Raw 1 (fw:1, sam:1) @@ -1843,82 +1872,82 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Raw 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Raw 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Raw multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Raw paired 1 (fw:1, sam:1) @@ -1926,10 +1955,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .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 +./bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 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 @@ -1938,30 +1967,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -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 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Raw paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -3 7 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 -3 7 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 14 -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) @@ -1969,47 +1998,45 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Tabbed 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --quiet -a --reads-per-batch 5 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Tabbed 7 (fw:1, sam:1) References: >0 @@ -2023,46 +2050,46 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim5 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 16 -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 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -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 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Tabbed paired 1 (fw:1, sam:1) @@ -2070,10 +2097,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --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 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 @@ -2082,30 +2109,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -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 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Tabbed paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 -3 7 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN Qseq 1 (fw:1, sam:1) @@ -2113,96 +2140,95 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 5052. Qseq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 5052. Qseq 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 14 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Qseq 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --trim3 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" Qseq multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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_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 +./bowtie2 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Qseq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Qseq paired 1 (fw:1, sam:1) @@ -2210,10 +2236,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 @@ -2222,10 +2248,10 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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) @@ -2233,39 +2259,39 @@ >0 GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 23 24 2M1I40M * 0 0 ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:42 YT:Z:UU Left-align deletion (fw:1, sam:1) References: >0 GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC -./bowtie2 --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 5 24 20M1D45M * 0 0 TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20^A0A44 YT:Z:UU Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) References: >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1192 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 3 42 38M = 1148 0 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UP r0 129 0 1148 1 42M = 3 0 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YT:Z:UP Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) @@ -2273,10 +2299,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1028 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -2284,10 +2310,10 @@ >0 TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG ./bowtie2-build --quiet .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 +./bowtie2 --fr --quiet --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:250 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 89 0 51 42 100M = 51 0 TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UP r0 165 0 51 0 * = 51 0 CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) @@ -2295,10 +2321,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --fr --quiet --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:290 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 3 1 38M = 246 285 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:CP r0 147 0 246 1 42M = 3 -285 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:CP MD:Z 1 (fw:1, sam:1) @@ -2306,10 +2332,10 @@ >0 CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 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: @@ -2325,135 +2351,135 @@ >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU MD:Z 2 (fw:0, sam:1) References: >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU MD:Z 3 (fw:1, sam:1) References: >0 CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU MD:Z 4 (fw:1, sam:1) References: >0 CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -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 .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 +./bowtie2 --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU Local alignment 1 (fw:0, sam:1) References: >0 TTGT -./bowtie2 --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 .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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 10 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --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 +./bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU r0 272 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU Local alignment 4 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --policy "SEED=0\;SEEDLEN=3\;IVAL=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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 12 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 7 -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) @@ -2461,10 +2487,10 @@ >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -2473,10 +2499,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -2497,10 +2523,10 @@ 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 +./bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 14 -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 @@ -2510,10 +2536,10 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 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 @@ -2544,10 +2570,10 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --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 +./bowtie2 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 339 0 270 255 19M = 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 @@ -2578,11 +2604,11 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --fr --quiet -M 1 --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 +./bowtie2 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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 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 @@ -2593,11 +2619,11 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 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 @@ -2609,187 +2635,187 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./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 +./bowtie2 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; no args (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -M 1 --no-discordant --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 13 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 5 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -2807,11 +2833,11 @@ 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 +./bowtie2 --no-contain --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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) @@ -2829,22 +2855,22 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-overlap --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -2852,153 +2878,153 @@ >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG ./bowtie2-build --quiet .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 +./bowtie2 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 .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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 2 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 16 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 4 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 5 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 6 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Q XS:i 1a (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./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 +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,3 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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: @@ -3014,131 +3040,131 @@ References: >0 TTGTTCGATTGTTCGA -./bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a I --mp 3,3 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a --ignore-quals (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a --ignore-quals (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --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 +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1b --ignore-quals (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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: @@ -3154,11 +3180,11 @@ References: >0 TTGTTCGATTGTTCGA -./bowtie2 --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 +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c --ignore-quals (fw:0, sam:1) References: @@ -3175,20 +3201,20 @@ >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./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 +./bowtie2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 73 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP (fw:0, sam:1) References: >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT -./bowtie2 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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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bowtie2-build --quiet .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 +./bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 217 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT -./bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 .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 +./bowtie2 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -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 +./bowtie2 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 8 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACGAACAA IIIIIIII YT:Z:UU XS:i 3a (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3b (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3b (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 6 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 2 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 .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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4a (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT -./bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5a (fw:1, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA ./bowtie2-build --quiet .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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5b (fw:0, sam:1) References: @@ -3440,125 +3466,125 @@ >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 1 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 11 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 16 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 5 -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 +./bowtie2 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP r0 147 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP SAM paired-end where both alignments start at the same offset (ff case) (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 24M = 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --rf --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 9 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 +./bowtie2 --rf --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 4 255 24M = 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP r0 131 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 73 0 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) @@ -3575,10 +3601,10 @@ References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -3588,11 +3614,11 @@ >1 GCTCGGAATTCGTGCTCCGNCCCGTACGGTT ./bowtie2-build --quiet .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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @SQ SN:1 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 2 -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: @@ -3611,19 +3637,19 @@ >0 GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU matchesRef regression 3 (fw:0, sam:1) References: >0 GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC -./bowtie2 --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 +./bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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: @@ -3632,11 +3658,11 @@ >1 CCTTGTTNTTAATGCTGCCTGGTTTNG ./bowtie2-build --quiet .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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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) @@ -3645,11 +3671,11 @@ 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 1 255 29S23M = 1 -68 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:-128 YT:Z:CP r0 163 0 1 255 45S15M = 1 68 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-128 XN:i:9 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:14T0 YS:i:-78 YT:Z:CP matchesRef regression 1 (fw:1, sam:1) @@ -3666,10 +3692,10 @@ References: >0 AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC -./bowtie2 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:61 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 11 -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: @@ -3678,11 +3704,11 @@ >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC ./bowtie2-build --quiet .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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -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 @@ -3693,11 +3719,11 @@ TTTATAAAAATATTTCCCCCCCC >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC -./bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -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 @@ -3707,80 +3733,80 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -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 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 +./bowtie2 -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --fr --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r1 99 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r1 147 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 -s 1 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 13 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -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 +./bowtie2 -s 2 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:0, 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 +./bowtie2 -s 2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r1 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: @@ -3795,142 +3821,142 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -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 +./bowtie2 -s 1 --trim5 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 3 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 1 --trim5 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 .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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 1 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -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 .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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 2 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r0 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 @@ -3938,10 +3964,10 @@ 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,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r0 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 @@ -3961,10 +3987,10 @@ References: >0 TTGTTCGT -./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" r0 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 @@ -3973,37 +3999,37 @@ References: >0 TTGTTCGT -./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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 --overhang --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 5 -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: @@ -4021,43 +4047,43 @@ 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 +./bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 1000 --local --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 1000 --local --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 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 1000 --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 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 @@ -4072,10 +4098,10 @@ 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 +./bowtie2 -X 1000 --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 @@ -4090,10 +4116,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 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 = 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 @@ -4108,10 +4134,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 @@ -4127,128 +4153,128 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --quiet .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 +./bowtie2 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -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: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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --local -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --local -X 150 --fr --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 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 +./bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --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 = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -4256,84 +4282,84 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --local -X 150 --fr --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 150 --fr --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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 -X 150 --local --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 +./bowtie2 -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --local --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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) @@ -4341,22 +4367,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -X 150 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 150 --fr --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 3 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 150 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --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 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) @@ -4364,22 +4390,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --local -X 150 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --local -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --local -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP U.M.1.G. Unpaired -M w/ 1 hit global (fw:1, sam:1) @@ -4387,68 +4413,68 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --local --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.L. Unpaired -m w/ 1 hit local (fw:0, sam:1) References: @@ -4464,156 +4490,156 @@ >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2-build --quiet .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 +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 2 --local --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -M 2 --local --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 2 --local --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 14 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 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 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 14 -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) @@ -4621,50 +4647,50 @@ >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -X 150 --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -X 150 --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 177 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -X 150 --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --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.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 16 -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 @@ -4674,10 +4700,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 @@ -4687,10 +4713,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -4700,10 +4726,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 3 -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 @@ -4714,10 +4740,10 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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) @@ -4743,20 +4769,20 @@ 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC ./bowtie2-build --quiet .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 +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 @@ -4777,10 +4803,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --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 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 @@ -4802,91 +4828,91 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 15 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 1 -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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU Gap penalties 3 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU Gap penalties 4 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 1 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU Gap penalties 5 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 2 -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: @@ -4902,39 +4928,39 @@ 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU Gap penalties 7 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet .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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 9 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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: @@ -4950,180 +4976,180 @@ >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 2 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:1, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 5 (fw:1, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU N filtering 5 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 6 (fw:0, sam:1) References: >0 GAGACTTTNTACGCATCGAANTATCGCTCTA -./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTTTGTTCGTTTG ./bowtie2-build --quiet .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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU (fw:0, sam:1) References: >0 TTTTGTTCGTTTG -./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 9 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU (fw:1, sam:1) References: >0 ACNCA ./bowtie2-build --quiet .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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (1) (fw:1, sam:1) References: >0 ACNCA -./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (2) (fw:1, sam:1) References: >0 ACNCANNNNNNNNCGNNNNNNNNCG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -5132,10 +5158,10 @@ References: >0 ACNCANNNNNNNNCGNNNNNNNNCG -./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -5145,10 +5171,10 @@ >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN ./bowtie2-build --quiet .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 +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -5159,10 +5185,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./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 +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -5173,10 +5199,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./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 +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -5187,10 +5213,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 @@ -5202,10 +5228,10 @@ >0 TTGTTYGT ./bowtie2-build --quiet .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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 6 -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) @@ -5213,38 +5239,38 @@ >0 ATAACCTTCG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 4 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU (fw:1, sam:1) References: >0 ATATGCCCCATGCCCCCCTCCG ./bowtie2-build --quiet .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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:22 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 12 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:22 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU Simple paired-end 13 (fw:1, sam:1) References: @@ -5300,10 +5326,10 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 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 @@ -5312,10 +5338,10 @@ References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC -./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 @@ -5325,20 +5351,20 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP Simple paired-end 11 (fw:0, sam:1) References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC -./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -5346,20 +5372,20 @@ >0 TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 28 -X 80 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 28 -X 80 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 28 -X 80 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --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 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) @@ -5367,22 +5393,22 @@ >0 CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -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 +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 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) @@ -5390,10 +5416,10 @@ >0 CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 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 @@ -5419,10 +5445,10 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 153 0 4 255 10M = 4 0 ATATATATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UP r0 101 0 4 0 * = 4 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP Simple paired-end 2; --no-mixed (fw:1, sam:1) @@ -5430,20 +5456,20 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --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 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) @@ -5451,10 +5477,10 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 131 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Simple paired-end 1 (fw:0, sam:1) @@ -5472,10 +5498,10 @@ >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 @@ -5496,10 +5522,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 @@ -5521,50 +5547,50 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet .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 +./bowtie2 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -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 .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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -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: @@ -5588,37 +5614,37 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 256 0 1 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 256 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU @@ -5629,10 +5655,10 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 272 0 9 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 272 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU @@ -5644,10 +5670,10 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 8 -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) @@ -5665,38 +5691,38 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 13 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -F 10,1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:12 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -F 10,1 --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 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 @@ -5709,11 +5735,11 @@ ./bowtie2-build --large-index --quiet .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 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:15 @SQ SN:1 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 0 0 1 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Align should not fail when multiple seqs are all Ns (fw:1, sam:1) References: @@ -5728,104 +5754,102 @@ Warning: Encountered reference sequence with only gaps Warning: Encountered reference sequence with only gaps Warning: Encountered reference sequence with only gaps -./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:15 @SQ SN:1 LN:15 @SQ SN:2 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:34 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -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 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -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 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP +./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG ABCDEDGHIJKLMNOP AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO +./bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO Error: Read 0 has more read characters than quality values. terminate called after throwing an instance of 'int' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Cline 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ +./bowtie2 --large-index --quiet -a --reads-per-batch 15 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) trim-to: trim from 5'-end (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim-to 5:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 5:12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 4 -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 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 3:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: trim from 3'-end (default) (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim-to 12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: invalid position (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim-to 4:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 4:12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: trim position must be either 3 or 5 Bowtie 2 version 2.5.4 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -5980,13 +6004,13 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 trim-to: invalid count (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: the number bases to trim must be at least 0 Bowtie 2 version 2.5.4 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -6141,67 +6165,67 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 Cline 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --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 Cline 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Cline 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" Cline multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 14 -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 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Cline paired 1 (fw:1, sam:1) @@ -6209,10 +6233,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII +./bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 @@ -6221,30 +6245,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Cline paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -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 16 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII +./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN Fastq 1 (fw:1, sam:1) @@ -6252,109 +6276,106 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 Fastq 3 (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 +./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 4 (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 +./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fastq 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fastq 6 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 10 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fastq 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 9 -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 6 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Fastq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz" Fastq multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 16 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq paired 1 (fw:1, sam:1) @@ -6362,10 +6383,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 @@ -6374,30 +6395,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --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 Fastq paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 11 -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) @@ -6405,130 +6426,128 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 15M * 0 0 CATCGATCAGTATCT IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -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 2 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz Error: reads file does not look like a FASTA file terminate called after throwing an instance of 'int' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fasta 6 (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 +./bowtie2 --large-index --quiet -a --reads-per-batch 6 -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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Fasta 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Fasta 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 16 -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 5 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 +./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -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) @@ -6536,10 +6555,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --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 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 @@ -6558,20 +6577,20 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --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 Fasta paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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) @@ -6579,10 +6598,10 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .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 +./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 2 (fw:1, sam:1) References: @@ -6597,19 +6616,19 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 11 -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: @@ -6624,37 +6643,37 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" Raw multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 --large-index -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Raw paired 1 (fw:1, sam:1) @@ -6662,10 +6681,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 @@ -6674,30 +6693,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -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 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Raw paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN Tabbed 1 (fw:1, sam:1) @@ -6705,19 +6724,19 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .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 +./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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: @@ -6732,73 +6751,71 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Tabbed 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./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' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Tabbed 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Tabbed 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" Tabbed multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Tabbed paired 1 (fw:1, sam:1) @@ -6806,10 +6823,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 @@ -6818,30 +6835,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Tabbed paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Tabbed paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN Qseq 1 (fw:1, sam:1) @@ -6849,96 +6866,95 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. 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 +./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values. terminate called after throwing an instance of 'int' -Aborted -(ERR): bowtie2-align exited with value 134 +(ERR): bowtie2-align died with signal 6 (ABRT) Qseq 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 4 --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 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -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 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Qseq multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Qseq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Qseq paired 1 (fw:1, sam:1) @@ -6946,10 +6962,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index 99 0 1 255 10M = 9 19 AGCATCGATC ABCBGACBCB AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP MachName_RunNum_Lane_Tile_10_10_Index 147 0 9 255 11M = 1 -19 TCAAAAACTGA ABCBCAGBCBA AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP @@ -6958,10 +6974,10 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -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) @@ -6978,30 +6994,30 @@ References: >0 GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC -./bowtie2 --large-index --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 13 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 5 24 20M1D45M * 0 0 TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20^A0A44 YT:Z:UU Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) References: >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1192 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 3 42 38M = 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) @@ -7009,10 +7025,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG ./bowtie2-build --large-index --quiet .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 +./bowtie2 --large-index --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1028 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 3 42 38M = 982 1021 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:DP r0 129 0 982 42 42M = 3 -1021 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:DP MREVERSE flag is set if mate does not align (fw:1, sam:1) @@ -7020,10 +7036,10 @@ >0 TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:250 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 8 -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) @@ -7031,10 +7047,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG ./bowtie2-build --large-index --quiet .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 +./bowtie2 --large-index --fr --quiet --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:290 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -7042,29 +7058,29 @@ >0 CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -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: @@ -7080,48 +7096,48 @@ >0 CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU MD:Z 4 (fw:1, sam:1) References: >0 CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --large-index --quiet .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 +./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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: @@ -7137,29 +7153,29 @@ >0 TTGA ./bowtie2-build --large-index --quiet .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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU Local alignment 2 (fw:0, sam:1) References: >0 TTGA -./bowtie2 --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 .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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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) @@ -7176,20 +7192,20 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 7 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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) @@ -7197,10 +7213,10 @@ >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -7209,10 +7225,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -7221,10 +7237,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -7246,10 +7262,10 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.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 +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 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 @@ -7280,10 +7296,10 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 83 0 169 1 19M = 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 @@ -7314,11 +7330,11 @@ 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 +./bowtie2 --large-index --fr --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 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 @@ -7329,11 +7345,11 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --large-index --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --large-index --fr --quiet -M 1 --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 Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --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 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 @@ -7345,44 +7361,44 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --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 +./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) @@ -7400,187 +7416,187 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --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-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-dovetail --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 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 4 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-overlap (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 +./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP Overlapping; --no-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-contain --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --no-overlap --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 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) @@ -7588,143 +7604,143 @@ >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG ./bowtie2-build --large-index --quiet .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 +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 .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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 2 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --large-index --ignore-quals --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 +./bowtie2 --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ignore-quals --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 3 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 4 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 8 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 5 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 6 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 .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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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: @@ -7740,141 +7756,141 @@ 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 +./bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a I --mp 3,3 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a --ignore-quals (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1b --ignore-quals (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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: @@ -7890,31 +7906,31 @@ 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 +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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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bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 15 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 289 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 .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 +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 1 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA ./bowtie2-build --large-index --quiet .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 +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU XS:i 1 (fw:0, sam:1) References: @@ -8014,10 +8030,10 @@ References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU XS:i 2 (fw:0, sam:1) References: @@ -8033,41 +8049,41 @@ >0 TTGTTCGATTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3c (fw:1, sam:1) References: @@ -8083,73 +8099,73 @@ References: >0 TTGTTCGATTGTTCGT -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4a (fw:1, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT ./bowtie2-build --large-index --quiet .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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 5 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --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 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --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 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 +./bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 .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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5a (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA -./bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --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 XS:i 5b (fw:1, sam:1) References: @@ -8165,76 +8181,76 @@ References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA -./bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 15 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU BWA-SW-like 1 (fw:0, sam:1) References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA -./bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 5 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU BWA-SW-like 2 (fw:0, sam:1) References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA -./bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 5 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -8251,70 +8267,70 @@ References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --large-index --rf --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 = 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 +./bowtie2 --large-index --rf --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP r0 163 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP SAM paired-end where both mates align 3 (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --large-index --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --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 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 +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 73 0 4 255 24M = 4 0 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YT:Z:UP r0 133 0 4 0 * = 4 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP SAM paired-end where neither mate aligns (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP SAM paired-end where both mates align, but discordantly (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YS:i:0 YT:Z:DP r0 129 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP matchesRef regression 4 (fw:1, sam:1) @@ -8324,11 +8340,11 @@ >1 GCTCGGAATTCGTGCTCCGNCCCGTACGGTT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @SQ SN:1 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU matchesRef regression 4 (fw:0, sam:1) References: @@ -8336,30 +8352,30 @@ CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC >1 GCTCGGAATTCGTGCTCCGNCCCGTACGGTT -./bowtie2 --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @SQ SN:1 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU matchesRef regression 3 (fw:1, sam:1) References: >0 GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC ./bowtie2-build --large-index --quiet .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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 12 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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: @@ -8368,11 +8384,11 @@ >1 CCTTGTTNTTAATGCTGCCTGGTTTNG ./bowtie2-build --large-index --quiet .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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP matchesRef regression 2 (fw:0, sam:1) @@ -8381,11 +8397,11 @@ GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG >1 CCTTGTTNTTAATGCTGCCTGGTTTNG -./bowtie2 --large-index --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -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) @@ -8393,19 +8409,19 @@ >0 AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:61 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU matchesRef regression 1 (fw:0, sam:1) References: >0 AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC -./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:61 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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: @@ -8414,11 +8430,11 @@ >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet .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 +./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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 -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 @@ -8429,11 +8445,11 @@ TTTATAAAAATATTTCCCCCCCC >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC -./bowtie2 --large-index -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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 113 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 113 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP @@ -8443,28 +8459,28 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 4 255 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --large-index -s 1 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" 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) @@ -8481,116 +8497,116 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 13 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --large-index -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 -u 1 --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 +./bowtie2 --large-index -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 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 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 .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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 9 -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 .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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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: @@ -8605,68 +8621,68 @@ References: >0 TTGTTCGT -./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 15 -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 @@ -8674,10 +8690,10 @@ 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -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 @@ -8685,10 +8701,10 @@ References: >0 TTGTTCGT -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r2 4 * 0 0 * * 0 0 GTTCGTA IIIIIII YT:Z:UU @@ -8697,10 +8713,10 @@ References: >0 TTGTTCGT -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r2 4 * 0 0 * * 0 0 TACGAAC IIIIIII YT:Z:UU @@ -8709,91 +8725,91 @@ References: >0 TTGTTCGT -./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 = 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 961 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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 1000 --local --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --local --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 1000 --local --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 961 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 @@ -8808,10 +8824,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 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 @@ -8826,10 +8842,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 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 @@ -8844,10 +8860,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 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 @@ -8863,128 +8879,128 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -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 +./bowtie2 --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 0 250 255 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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -M 1 -X 150 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 +./bowtie2 --large-index --fr --quiet -M 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index --fr --quiet -M 1 --local -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -M 1 --local -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -8992,84 +9008,84 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 +./bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.M.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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 --large-index -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 +./bowtie2 --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --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 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 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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) @@ -9077,22 +9093,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 3 -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 +./bowtie2 --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 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) @@ -9100,22 +9116,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -9123,11 +9139,11 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) References: @@ -9143,57 +9159,57 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 11 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 11 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --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: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: @@ -9210,107 +9226,107 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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.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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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: @@ -9336,20 +9352,20 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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) @@ -9357,50 +9373,50 @@ >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 134 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 134 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 9 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 219 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 @@ -9410,10 +9426,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 @@ -9423,10 +9439,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -k 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 8 -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 @@ -9450,49 +9466,49 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU r0 256 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 +./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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --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 +./bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 @@ -9513,10 +9529,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 11 -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 +./bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 11 -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -9538,148 +9554,148 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU Gap penalties 1 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU Gap penalties 2 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU 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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 5 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 6 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 --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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU Gap penalties 5 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU Gap penalties 6 (fw:1, sam:1) References: >0 ATTGTTCGTTTGTTCGTA ./bowtie2-build --large-index --quiet .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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 2 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 10 -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 .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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 +./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU N filtering 1 (fw:1, sam:1) References: >0 GAGACTTTATACGCATCGAACTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU N filtering 2 (fw:1, sam:1) References: @@ -9695,10 +9711,10 @@ References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:1, sam:1) References: @@ -9714,48 +9730,48 @@ References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 4 (fw:1, sam:1) References: >0 GAGACTTTNTACGCATCGAACTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 5 (fw:1, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2-build --large-index --quiet .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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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: @@ -9771,95 +9787,95 @@ 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTTTGTTCGTTTG ./bowtie2-build --large-index --quiet .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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU (fw:0, sam:1) References: >0 TTTTGTTCGTTTG -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 14 -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 .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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 .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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (1) (fw:0, sam:1) References: >0 ACNCA -./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (2) (fw:1, sam:1) References: >0 ACNCANNNNNNNNCGNNNNNNNNCG ./bowtie2-build --large-index --quiet .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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 24 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -9881,10 +9897,10 @@ >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN ./bowtie2-build --large-index --quiet .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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 @@ -9895,10 +9911,10 @@ 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 +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 @@ -9909,10 +9925,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -9923,10 +9939,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 @@ -9938,10 +9954,10 @@ >0 TTGTTYGT ./bowtie2-build --large-index --quiet .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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 6 -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) @@ -9949,48 +9965,48 @@ >0 ATAACCTTCG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 15 -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 .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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:22 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 2 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:22 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 5 -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 .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz +./bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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 @@ -10011,10 +10027,10 @@ References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC -./bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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 +./bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" r0 113 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 113 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP @@ -10036,10 +10052,10 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./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,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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,.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 @@ -10048,10 +10064,10 @@ 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 +./bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.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 @@ -10061,20 +10077,20 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet .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 +./bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP Simple paired-end 11 (fw:0, sam:1) References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC -./bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -I 0 -X 36 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --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 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) @@ -10082,20 +10098,20 @@ >0 TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --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 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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 113 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP Simple paired-end 9 (fw:1, sam:1) @@ -10103,22 +10119,22 @@ >0 CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --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 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -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:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 = 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) @@ -10126,10 +10142,10 @@ >0 CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC ./bowtie2-build --large-index --quiet .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 +./bowtie2 --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 4 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 @@ -10140,10 +10156,10 @@ References: >0 CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC -./bowtie2 --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --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 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 @@ -10155,10 +10171,10 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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) @@ -10166,20 +10182,20 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --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 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 +./bowtie2 --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP Simple paired-end 1 (fw:1, sam:1) @@ -10187,20 +10203,20 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -I 0 -X 50 --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --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 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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 179 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP (fw:1, sam:1) @@ -10208,10 +10224,10 @@ >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 0 0 24 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -10232,10 +10248,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --large-index --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 @@ -10257,59 +10273,59 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 .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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: @@ -10324,37 +10340,37 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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 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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 256 0 1 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 256 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU @@ -10365,10 +10381,10 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.4 CL:"/build/reproducible-path/bowtie2-2.5.4/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 @@ -10433,8 +10449,8 @@ make[1]: Leaving directory '/build/reproducible-path/bowtie2-2.5.4' dh_md5sums dh_builddeb -dpkg-deb: building package 'bowtie2' in '../bowtie2_2.5.4-1_arm64.deb'. dpkg-deb: building package 'bowtie2-dbgsym' in '../bowtie2-dbgsym_2.5.4-1_arm64.deb'. +dpkg-deb: building package 'bowtie2' in '../bowtie2_2.5.4-1_arm64.deb'. dpkg-deb: building package 'bowtie2-examples' in '../bowtie2-examples_2.5.4-1_all.deb'. dpkg-genbuildinfo --build=binary -O../bowtie2_2.5.4-1_arm64.buildinfo dpkg-genchanges --build=binary -O../bowtie2_2.5.4-1_arm64.changes @@ -10443,12 +10459,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2124697/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2124697/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/718729 and its subdirectories -I: Current time: Sat Jan 17 20:10:57 -12 2026 -I: pbuilder-time-stamp: 1768723857 +I: removing directory /srv/workspace/pbuilder/2124697 and its subdirectories +I: Current time: Sun Jan 18 22:22:12 +14 2026 +I: pbuilder-time-stamp: 1768724532