Diff of the two buildlogs: -- --- b1/build.log 2023-04-11 14:23:53.208722948 +0000 +++ b2/build.log 2023-04-11 15:18:52.802656692 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 11 01:32:30 -12 2023 -I: pbuilder-time-stamp: 1681219950 +I: Current time: Tue May 14 10:46:56 +14 2024 +I: pbuilder-time-stamp: 1715633216 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration @@ -16,7 +16,7 @@ I: copying [./bowtie2_2.5.0.orig.tar.gz] I: copying [./bowtie2_2.5.0-3.debian.tar.xz] I: Extracting source -gpgv: Signature made Tue Jan 17 04:42:01 2023 -12 +gpgv: Signature made Wed Jan 18 06:42:01 2023 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -37,11 +37,20 @@ 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/30247/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/29054/tmp/hooks/D01_modify_environment starting +debug: Running on codethink9-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 +lrwxrwxrwx 1 root root 4 Jan 6 2023 /bin/sh -> dash +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/29054/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/29054/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' + 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=8' @@ -51,38 +60,38 @@ IFS=' ' LANG='C' - LANGUAGE='en_US:en' + LANGUAGE='nl_BE:nl' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' + 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' - PPID='30247' + PPID='29054' PS1='# ' PS2='> ' 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.7YguTcU7/pbuilderrc_AsmF --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7YguTcU7/b1 --logfile b1/build.log bowtie2_2.5.0-3.dsc' + 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.7YguTcU7/pbuilderrc_WQnD --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.7YguTcU7/b2 --logfile b2/build.log --extrapackages usrmerge bowtie2_2.5.0-3.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' + TZ='/usr/share/zoneinfo/Etc/GMT-14' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a - Linux codethink14-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux + Linux i-capture-the-hostname 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 9 22:24 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/30247/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 12 06:48 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/29054/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -197,7 +206,7 @@ Get: 57 http://deb.debian.org/debian bookworm/main arm64 pandoc-data all 2.17.1.1-1.1 [417 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 pandoc arm64 2.17.1.1-1.1 [29.0 MB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] -Fetched 55.6 MB in 1s (51.2 MB/s) +Fetched 55.6 MB in 4s (12.5 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 ... 19616 files and directories currently installed.) @@ -451,8 +460,17 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +usrmerge is already the newest version (35). +0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/bowtie2-2.5.0/ && 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_2.5.0-3_source.changes +I: user script /srv/workspace/pbuilder/29054/tmp/hooks/A99_set_merged_usr starting +Re-configuring usrmerge... +I: user script /srv/workspace/pbuilder/29054/tmp/hooks/A99_set_merged_usr finished +hostname: Temporary failure in name resolution +I: Running cd /build/bowtie2-2.5.0/ && 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_2.5.0-3_source.changes dpkg-buildpackage: info: source package bowtie2 dpkg-buildpackage: info: source version 2.5.0-3 dpkg-buildpackage: info: source distribution unstable @@ -463,14 +481,14 @@ dh clean dh_auto_clean make -j8 clean -make[1]: Entering directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt binnengegaan rm -f bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-build-s-debug bowtie2-build-l-debug bowtie2-align-s-debug bowtie2-align-l-debug bowtie2-inspect-s-debug bowtie2-inspect-l-debug \ bowtie2-build-s.exe bowtie2-build-l.exe bowtie2-align-s.exe bowtie2-align-l.exe bowtie2-inspect-s.exe bowtie2-inspect-l.exe bowtie2-build-s-debug.exe bowtie2-build-l-debug.exe bowtie2-align-s-debug.exe bowtie2-align-l-debug.exe bowtie2-inspect-s-debug.exe bowtie2-inspect-l-debug.exe \ bowtie2-*.zip rm -f core.* .tmp.head rm -rf *.dSYM rm -rf .tmp -make[1]: Leaving directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt verlaten dh_clean debian/rules binary dh binary @@ -478,10 +496,10 @@ dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build -make[1]: Entering directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt binnengegaan LD_PRELOAD= dh_auto_build -- EXTRA_FLAGS="-std=c++98 -Wl,-z,relro -Wl,-z,now" NO_TBB=1 POPCNT_CAPABILITY= HOSTNAME=reproducible-hostname make -j8 "INSTALL=install --strip-program=true" "EXTRA_FLAGS=-std=c++98 -Wl,-z,relro -Wl,-z,now" NO_TBB=1 POPCNT_CAPABILITY= HOSTNAME=reproducible-hostname -make[2]: Entering directory '/build/bowtie2-2.5.0' +make[2]: Map '/build/bowtie2-2.5.0' wordt binnengegaan g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -g -O2 -ffile-prefix-map=/build/bowtie2-2.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`LC_ALL=C date -u -d@1673968535`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -g -O2 -ffile-prefix-map=/build/bowtie2-2.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -DNDEBUG -Wall \ -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party \ @@ -556,15 +574,15 @@ bt2_search.cpp:4605:20: note: call to ‘int closedir(DIR*)’ here 4605 | if(closedir(dir) != 0) { | ~~~~~~~~^~~~~ -make[2]: Leaving directory '/build/bowtie2-2.5.0' +make[2]: Map '/build/bowtie2-2.5.0' wordt verlaten dh_auto_build -- doc/manual.html make -j8 "INSTALL=install --strip-program=true" doc/manual.html -make[2]: Entering directory '/build/bowtie2-2.5.0' -make[2]: 'doc/manual.html' is up to date. -make[2]: Leaving directory '/build/bowtie2-2.5.0' -make[1]: Leaving directory '/build/bowtie2-2.5.0' +make[2]: Map '/build/bowtie2-2.5.0' wordt binnengegaan +make[2]: 'doc/manual.html' is up-to-date. +make[2]: Map '/build/bowtie2-2.5.0' wordt verlaten +make[1]: Map '/build/bowtie2-2.5.0' wordt verlaten debian/rules override_dh_auto_test -make[1]: Entering directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt binnengegaan LD_PRELOAD= /usr/bin/make EXTRA_FLAGS="-std=c++98 -Wl,-z,relro -Wl,-z,now" NO_TBB=1 POPCNT_CAPABILITY= \ bowtie2-build-s-debug \ bowtie2-build-l-debug \ @@ -572,7 +590,7 @@ bowtie2-align-l-debug \ bowtie2-inspect-s-debug \ bowtie2-inspect-l-debug -make[2]: Entering directory '/build/bowtie2-2.5.0' +make[2]: Map '/build/bowtie2-2.5.0' wordt binnengegaan g++ -O0 -g3 -DCOMPILER_OPTIONS="\"-O0 -g3 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1\"" -g -O2 -ffile-prefix-map=/build/bowtie2-2.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1 \ -fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat BOWTIE2_VERSION`\"" -DBUILD_HOST="\"${HOSTNAME:-`hostname`}\"" -DBUILD_TIME="\"`LC_ALL=C date -u -d@1673968535`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party -g -O2 -ffile-prefix-map=/build/bowtie2-2.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DBOWTIE2 -Wall \ -Wdate-time -D_FORTIFY_SOURCE=2 -Ithird_party \ @@ -645,9 +663,9 @@ -o bowtie2-inspect-l-debug bt2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_locks.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp \ -Wl,-z,relro -Wl,-z,now -lpthread -lz -make[2]: Leaving directory '/build/bowtie2-2.5.0' +make[2]: Map '/build/bowtie2-2.5.0' wordt verlaten LD_PRELOAD= make -j1 test -make[2]: Entering directory '/build/bowtie2-2.5.0' +make[2]: Map '/build/bowtie2-2.5.0' wordt binnengegaan eval `perl -I /build/bowtie2-2.5.0/.tmp/lib/perl5 -Mlocal::lib=/build/bowtie2-2.5.0/.tmp` ; \ sh ./scripts/test/simple_tests.sh Attempting to create directory /build/bowtie2-2.5.0/.tmp @@ -658,20 +676,20 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -F 10,9 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,9 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU seq1_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 12 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 @@ -679,38 +697,38 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -F 10,9 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,9 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -F 10,9 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,9 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 15 -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 14 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,9 -u 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 13 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 -F 10,1 --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:12 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 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 @@ -723,11 +741,11 @@ ./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 1 -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:15 @SQ SN:1 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -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: @@ -742,41 +760,41 @@ 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 16 -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:15 @SQ SN:1 LN:15 @SQ SN:2 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -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 10 -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:34 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 0 0 0 18 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 2 (fw:1, sam:1) References: @@ -791,7 +809,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO +./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO Error: Read 0 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted @@ -800,7 +818,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ +./bowtie2 --quiet -a --reads-per-batch 13 -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 @@ -809,37 +827,37 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim-to 5:12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim-to 5:12 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 11 -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 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: trim from 3'-end (default) (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim-to 12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim-to 12 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: 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 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: trim position must be either 3 or 5 Bowtie 2 version 2.5.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -992,13 +1010,13 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/bowtie2-2.5.0/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/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 10 -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 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim-to 5:-12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: the number bases to trim must be at least 0 Bowtie 2 version 2.5.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -1151,26 +1169,26 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 Cline 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Cline 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim5 16 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --trim5 16 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 10 -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: @@ -1184,34 +1202,34 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --quiet -a --reads-per-batch 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Cline multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 -u 1 --quiet -a --reads-per-batch 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG +./bowtie2 -u 2 --quiet -a --reads-per-batch 6 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 6 -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) @@ -1219,10 +1237,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII +./bowtie2 --quiet -a --reads-per-batch 12 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 @@ -1231,30 +1249,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Cline paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 -u 1 --quiet -a --reads-per-batch 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -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 11 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII +./bowtie2 -3 7 --quiet -a --reads-per-batch 2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 2 -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) @@ -1262,34 +1280,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 9 -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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 2 (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 6 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 3 (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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 16 -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 Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted @@ -1298,7 +1316,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --quiet -a --reads-per-batch 10 -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 @@ -1307,7 +1325,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' Aborted @@ -1316,36 +1334,36 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Fastq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --trim5 16 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 6 -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 5 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz" Fastq multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 14 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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) @@ -1361,10 +1379,10 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq paired 1 (fw:1, sam:1) @@ -1372,10 +1390,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 @@ -1384,30 +1402,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Fastq paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -u 1 --quiet -a --reads-per-batch 6 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Fastq paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -3 7 --quiet -a --reads-per-batch 3 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" r0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP r0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN Fasta 1 (fw:1, sam:1) @@ -1415,34 +1433,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 12 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 15 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 16 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 Fasta 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz Error: reads file does not look like a FASTA file terminate called after throwing an instance of 'int' Aborted @@ -1451,7 +1469,7 @@ 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 1 -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 @@ -1460,85 +1478,85 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 4 --quiet -a --reads-per-batch 16 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Fasta 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --trim3 16 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Fasta 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -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 7 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 1 (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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 12 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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) @@ -1546,10 +1564,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --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 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 @@ -1568,20 +1586,20 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -u 1 --quiet -a --reads-per-batch 5 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Fasta paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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) @@ -1589,82 +1607,82 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 5 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 (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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Raw 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --trim3 16 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 16 -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 12 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -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 4 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 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 8 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --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 multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --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 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) @@ -1672,10 +1690,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP @@ -1694,20 +1712,20 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -u 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 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Raw paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -3 7 --quiet -a --reads-per-batch 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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) @@ -1715,19 +1733,19 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 3 (fw:1, sam:1) References: @@ -1742,7 +1760,7 @@ 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 11 -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 @@ -1751,7 +1769,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz Error: Read r0 has more quality values than read characters. terminate called after throwing an instance of 'int' Aborted @@ -1760,55 +1778,55 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Tabbed 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --trim5 16 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Tabbed 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 5 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 5 -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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Tabbed multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 1 --quiet -a --reads-per-batch 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Tabbed paired 1 (fw:1, sam:1) @@ -1816,10 +1834,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --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 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 @@ -1838,20 +1856,20 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -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 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 -3 7 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 15 -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) @@ -1859,37 +1877,37 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz Error: Read MachName_RunNum_Lane_Tile_X_Y_Index/0 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted @@ -1898,38 +1916,38 @@ 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 4 --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 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 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --trim3 16 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 2 -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 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" Qseq multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_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) @@ -1945,10 +1963,10 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -u 2 --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 paired 1 (fw:1, sam:1) @@ -1956,10 +1974,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 7 -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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 @@ -1968,10 +1986,10 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -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) @@ -1988,30 +2006,30 @@ References: >0 GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC -./bowtie2 --quiet --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet --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:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 15 -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 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet --reads-per-batch 1 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1192 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 3 42 38M = 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) @@ -2019,10 +2037,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG ./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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1028 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 3 42 38M = 982 1021 GCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YS:i:0 YT:Z:DP r0 129 0 982 42 42M = 3 -1021 ACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YS:i:0 YT:Z:DP MREVERSE flag is set if mate does not align (fw:1, sam:1) @@ -2030,10 +2048,10 @@ >0 TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG ./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 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:250 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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) @@ -2041,10 +2059,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --fr --quiet --reads-per-batch 10 -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:290 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/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 99 0 3 1 38M = 80 119 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 80 1 42M = 3 -119 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) @@ -2052,154 +2070,154 @@ >0 CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU MD:Z 1 (fw:0, sam:1) References: >0 CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./bowtie2 --quiet -a --reads-per-batch 13 -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:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU MD:Z 2 (fw:1, sam:1) References: >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -a --reads-per-batch 4 -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:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 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 4 -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:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 14 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU MD:Z 4 (fw:0, sam:1) References: >0 CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./bowtie2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 --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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 8 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --policy "MIN=L,1.0,0.75" --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 3 -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 15 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU Local alignment 2 (fw:0, sam:1) References: >0 TTGA -./bowtie2 --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 5 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU r0 256 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU Local alignment 3 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 4 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/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 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 5 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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) @@ -2207,10 +2225,10 @@ >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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -2231,10 +2249,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --min-score C,-24,0 -L 4 --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:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -2243,10 +2261,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -2256,10 +2274,10 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 99 0 104 1 19M = 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 r0 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP @@ -2290,10 +2308,10 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./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 +./bowtie2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP @@ -2339,11 +2357,11 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 83 0 68 1 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 163 0 3 1 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 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 @@ -2355,22 +2373,22 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --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 +./bowtie2 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 1 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant (fw:1, sam:1) @@ -2388,209 +2406,209 @@ 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 8 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 16 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-overlap (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --no-overlap --ff --quiet -M 1 --reads-per-batch 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Overlapping; no args (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --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 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 1 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP Overlapping; --no-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --no-dovetail --ff --quiet -M 1 --reads-per-batch 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP Overlapping; --no-contain (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --no-contain --ff --quiet -M 1 --reads-per-batch 15 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP Overlapping; --no-contain (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --no-contain --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 --no-contain --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-contain --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP Overlapping; --no-overlap (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --no-overlap --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-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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-overlap --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 11 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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) @@ -2598,183 +2616,183 @@ >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU Scoring params 1 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG -./bowtie2 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -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 3 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 11 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --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:-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 8 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 3 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --ignore-quals --rfg 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -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 6 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 4 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 5 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -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 11 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 3 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 6 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 11 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,6 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 6 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 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: @@ -2790,51 +2808,51 @@ 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a I --mp 3,6 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 7 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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" 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 13 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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: @@ -2850,11 +2868,11 @@ References: >0 TTGTTCGATTGTTCGA -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1b --ignore-quals (fw:1, sam:1) References: @@ -2880,61 +2898,61 @@ References: >0 TTGTTCGATTGTTCGA -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c --ignore-quals (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c --ignore-quals (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU (fw:1, sam:1) References: >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT ./bowtie2-build --quiet .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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 73 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP (fw:0, sam:1) References: >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT -./bowtie2 --fr --quiet -a --reads-per-batch 4 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 137 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP r0 69 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP (fw:1, sam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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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 217 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT -./bowtie2 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -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 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 1 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU XS:i 2 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3b (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 1 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3b (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 5 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3c (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 4 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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" 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4b (fw:0, sam:1) References: @@ -3145,60 +3163,60 @@ >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 10 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5a (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA -./bowtie2 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 5 -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 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:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --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 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 3 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5b (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA -./bowtie2 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 11 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU BWA-SW-like 1 (fw:1, sam:1) References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --bwa-sw-like --quiet -a --reads-per-batch 12 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --bwa-sw-like --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:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 7 -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: @@ -3213,118 +3231,118 @@ References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA -./bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 8 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --bwa-sw-like -i 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:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 1 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP r0 131 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --rf --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --rf --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP r0 163 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP SAM paired-end where both mates align 1 (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 4 255 24M = 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --rf --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --rf --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP r0 163 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP SAM paired-end where both mates align 3 (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 24M = 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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 73 0 4 255 24M = 4 0 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YT:Z:UP r0 133 0 4 0 * = 4 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP SAM paired-end where neither mate aligns (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP SAM paired-end where both mates align, but discordantly (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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) @@ -3334,11 +3352,11 @@ >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 13 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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: @@ -3346,30 +3364,30 @@ CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC >1 GCTCGGAATTCGTGCTCCGNCCCGTACGGTT -./bowtie2 --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 8 -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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GCGAGTGAGGGGCATGAAGCAAGCGGGGCGTGAAGACCCCGAGAGCGGGGGCGGGGACAACGGATGGGGAGGGGTGCGAGCCGACAAAGGGAGGGTGAGGGGCATGACGCAAACGGGGAGTGACGACCGGCGGGCGGGGGCGGGGACAACGGATGGGGATGGGTGGGAGCCGACAAGGGAGGGGTGCAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU matchesRef regression 3 (fw:1, sam:1) References: >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 4 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" r0 16 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU matchesRef regression 3 (fw:0, sam:1) References: >0 GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC -./bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --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:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 2 -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: @@ -3378,11 +3396,11 @@ >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 3 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -3391,11 +3409,11 @@ 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 14 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 89 0 1 255 29S23M = 1 0 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YT:Z:UP r0 165 0 1 0 * = 1 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP matchesRef regression 1 (fw:1, sam:1) @@ -3403,19 +3421,19 @@ >0 AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --overhang --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:61 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU matchesRef regression 1 (fw:0, sam:1) References: >0 AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC -./bowtie2 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --overhang --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:61 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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: @@ -3424,11 +3442,11 @@ >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 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 @@ -3439,11 +3457,11 @@ 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 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:23 @SQ SN:1 LN:28 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -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 @@ -3453,230 +3471,230 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --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" 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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 2 --fr --quiet -a --reads-per-batch 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 +./bowtie2 -s 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 2 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 2 --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" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 2 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 -s 2 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 -u 1 --quiet -a --reads-per-batch 6 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 0 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 -s 1 --trim3 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 -s 1 --trim3 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 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 13 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 4 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU (fw:0, sam:1) References: >0 TGC -./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 7 -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 8 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -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 14 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 11 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 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 8 -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:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --overhang --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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" r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 14 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU r2 0 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU @@ -3684,10 +3702,10 @@ 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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r0 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 @@ -3695,10 +3713,10 @@ References: >0 TTGTTCGT -./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz +./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" r0 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 @@ -3707,10 +3725,10 @@ References: >0 TTGTTCGT -./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.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 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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.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 @@ -3719,28 +3737,28 @@ 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 +./bowtie2 --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:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --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: @@ -3756,54 +3774,54 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 724 1 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 -X 1000 --fr --quiet -M 5 --reads-per-batch 11 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.M.58.L.b Unpaired -M 5 w/ 8 hits local, but mate #1 has just 1 (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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" r0 99 0 13 1 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 724 1 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.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 10 -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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.k.58.G.b Unpaired -k 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 -X 1000 --fr --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 1000 --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 355 0 13 255 33M = 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 @@ -3818,10 +3836,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 -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 -X 1000 --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP @@ -3836,10 +3854,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 355 0 13 255 33M = 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 @@ -3854,10 +3872,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP @@ -3873,64 +3891,64 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -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 +./bowtie2 -X 150 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.M.22.G. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -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 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.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 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 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 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 --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 +./bowtie2 --local -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 -X 150 --fr --quiet -k 1 --reads-per-batch 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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) @@ -3947,54 +3965,54 @@ 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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --fr --quiet -M 1 -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 1 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 1 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --fr --quiet -M 1 --local -X 150 --reads-per-batch 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.M.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 16 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 0 316 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) @@ -4002,20 +4020,20 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --fr --quiet -k 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 5 -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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) @@ -4032,54 +4050,54 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --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 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.M.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 9 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 16 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 15 -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 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:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --local --fr --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 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) @@ -4087,22 +4105,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 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.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 5 -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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 553 1 28M = 487 -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 0 487 1 33M = 553 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) @@ -4110,22 +4128,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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" r0 99 0 961 1 33M = 1027 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 1027 1 28M = 961 -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 14 -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 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:1906 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local -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 83 0 1264 1 28M = 1198 -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 1198 1 33M = 1264 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) @@ -4133,184 +4151,184 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --quiet -M 1 --reads-per-batch 4 -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:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 7 -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:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --local --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 --local --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 5 -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:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 7 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 6 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 2 --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.22.L. Unpaired -M 2 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -M 2 --local --reads-per-batch 3 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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: @@ -4326,40 +4344,40 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 2 --reads-per-batch 3 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -k 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) @@ -4367,50 +4385,50 @@ >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 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:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 5 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -M 5 --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:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 10 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 5 --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:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 10 -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 @@ -4420,10 +4438,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 @@ -4433,10 +4451,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 304 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU @@ -4446,10 +4464,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --local --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --local --quiet -k 5 --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:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -4460,49 +4478,49 @@ >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 1 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU r0 256 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 6 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU r0 272 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 1 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCAT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 9 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 0 0 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 @@ -4523,10 +4541,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 @@ -4548,243 +4566,243 @@ >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 15 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 1 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -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 2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU Gap penalties 3 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU Gap penalties 3 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU Gap penalties 4 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 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=30,16\;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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU Gap penalties 4 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU Gap penalties 5 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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: >0 ATTGTTCGTTTGTTCGTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU Gap penalties 6 (fw:0, sam:1) References: >0 ATTGTTCGTTTGTTCGTA -./bowtie2 --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 +./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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU Gap penalties 7 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --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 8 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 10 -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 11 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 12 -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 12 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU N filtering 1 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAACTATCGCTCTA -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU N filtering 2 (fw:1, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 2 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 4 (fw:0, sam:1) References: >0 GAGACTTTNTACGCATCGAACTATCGCTCTA -./bowtie2 --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 6 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 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 10 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU N filtering 5 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 14 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 12 -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 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 6 (fw:0, sam:1) References: >0 GAGACTTTNTACGCATCGAANTATCGCTCTA -./bowtie2 --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 1 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU (fw:1, sam:1) References: @@ -4800,29 +4818,29 @@ 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 8 -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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTT ./bowtie2-build --quiet .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 3 -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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 16 -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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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: @@ -4838,10 +4856,10 @@ References: >0 ACNCA -./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 +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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: @@ -4856,20 +4874,20 @@ References: >0 ACNCA -./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 8 -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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -4878,10 +4896,10 @@ References: >0 ACNCANNNNNNNNCGNNNNNNNNCG -./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 @@ -4891,10 +4909,10 @@ >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 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -4919,10 +4937,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -4933,10 +4951,10 @@ 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 @@ -4948,10 +4966,10 @@ >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 1 -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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 5 -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) @@ -4959,48 +4977,48 @@ >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 13 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 16 -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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -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 1 -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 6 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 6 -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 1 -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 8 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU Simple paired-end 13 (fw:1, sam:1) References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz +./bowtie2 -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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 @@ -5046,10 +5064,10 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 -I 0 -X 36 --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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,.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 @@ -5058,10 +5076,10 @@ 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 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 @@ -5071,20 +5089,20 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 36 --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 36 --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:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 36 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 -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 14 -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 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:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 -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) @@ -5092,20 +5110,20 @@ >0 TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 28 -X 80 --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 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:41 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 113 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP Simple paired-end 9 (fw:1, sam:1) @@ -5113,22 +5131,22 @@ >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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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 -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 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -5136,10 +5154,10 @@ >0 CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 11 -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 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 @@ -5150,10 +5168,10 @@ References: >0 CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC -./bowtie2 -I 0 -X 80 --fr --quiet -a --reads-per-batch 11 -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 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:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --fr --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 80 --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 83 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 163 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 339 0 60 255 10M = 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 @@ -5165,10 +5183,10 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 13 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --ff --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 153 0 4 255 10M = 4 0 ATATATATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UP r0 101 0 4 0 * = 4 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP Simple paired-end 2; --no-mixed (fw:1, sam:1) @@ -5176,20 +5194,20 @@ >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 16 -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 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:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 13 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP Simple paired-end 1 (fw:1, sam:1) @@ -5197,20 +5215,20 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 -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 -I 0 -X 50 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 131 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Simple paired-end 1 (fw:0, sam:1) References: >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC -./bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 -I 0 -X 50 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -5218,10 +5236,10 @@ >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./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 +./bowtie2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 0 0 4 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -5242,10 +5260,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --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" 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 @@ -5267,77 +5285,77 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --quiet -M 1 --reads-per-batch 3 -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:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --quiet -a --reads-per-batch 14 -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:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --policy SEED=0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: @@ -5352,19 +5370,19 @@ 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 @@ -5375,10 +5393,10 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 10 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 16 -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 @@ -5390,20 +5408,20 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug -F 10,9 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 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 --debug -F 10,9 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug -F 10,9 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 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 @@ -5411,38 +5429,38 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -F 10,9 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug -F 10,9 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -F 10,9 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug -F 10,9 -s 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 3 -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 --debug -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -F 10,1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug -F 10,1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:12 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -F 10,1 --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_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 @@ -5455,11 +5473,11 @@ ./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 --debug --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --debug --quiet -a --reads-per-batch 5 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -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: @@ -5474,56 +5492,56 @@ Warning: Encountered reference sequence with only gaps Warning: Encountered reference sequence with only gaps Warning: Encountered reference sequence with only gaps -./bowtie2 --debug --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --debug --quiet -a --reads-per-batch 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 --debug --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP +./bowtie2 --debug --quiet -a --reads-per-batch 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -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 --debug --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO +./bowtie2 --debug --quiet -a --reads-per-batch 4 -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 @@ -5532,7 +5550,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ +./bowtie2 --debug --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ Error: Read 0 has more quality values than read characters. terminate called after throwing an instance of 'int' Aborted @@ -5541,37 +5559,37 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim-to 5:12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --trim-to 5:12 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 1 -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 --debug --trim-to 3:12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --trim-to 3:12 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim-to 3:12 --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: trim from 3'-end (default) (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim-to 12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --trim-to 4:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --trim-to 4:12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: trim position must be either 3 or 5 Bowtie 2 version 2.5.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -5724,13 +5742,13 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 7 -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 --debug --trim-to 5:-12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --trim-to 5:-12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: the number bases to trim must be at least 0 Bowtie 2 version 2.5.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -5883,67 +5901,67 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII (ERR): bowtie2-align exited with value 1 Cline 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Cline 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Cline 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" Cline multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --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 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 --debug -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG +./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -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) @@ -5951,10 +5969,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 @@ -5963,30 +5981,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Cline paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Cline paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -3 7 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII +./bowtie2 --debug -3 7 --quiet -a --reads-per-batch 8 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 8 -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) @@ -5994,34 +6012,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted @@ -6030,7 +6048,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted @@ -6039,7 +6057,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' Aborted @@ -6048,36 +6066,36 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Fastq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim5 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --trim5 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Fastq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz" Fastq multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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) @@ -6093,10 +6111,10 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq paired 1 (fw:1, sam:1) @@ -6104,10 +6122,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 13 -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 @@ -6116,30 +6134,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -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 --debug -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --debug -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -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 --debug -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --debug -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 10 -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) @@ -6147,34 +6165,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 15M * 0 0 CATCGATCAGTATCT IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --quiet -a --reads-per-batch 4 -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 @@ -6183,7 +6201,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --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 @@ -6192,85 +6210,85 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 3 -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 --debug --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --trim3 16 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 5 -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 --debug -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" Fasta multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 --debug -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta paired 1 (fw:1, sam:1) @@ -6278,10 +6296,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --debug --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP @@ -6290,30 +6308,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP Fasta paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Fasta paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -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 --debug -3 7 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 1 -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) @@ -6321,10 +6339,10 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 2 (fw:1, sam:1) References: @@ -6339,28 +6357,28 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 8 -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 --debug --trim3 16 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --trim3 16 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 14 -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: @@ -6374,29 +6392,29 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 --debug -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Raw paired 1 (fw:1, sam:1) @@ -6404,10 +6422,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --debug --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP @@ -6426,10 +6444,10 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Raw paired 4 (fw:1, sam:1) @@ -6447,34 +6465,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted @@ -6483,7 +6501,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --quiet -a --reads-per-batch 7 -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 @@ -6492,55 +6510,55 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim3 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 4 -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 --debug --trim5 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Tabbed 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" Tabbed multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Tabbed multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Tabbed paired 1 (fw:1, sam:1) @@ -6548,10 +6566,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 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 @@ -6560,30 +6578,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -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 --debug -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug -3 7 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 11 -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) @@ -6591,37 +6609,37 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --quiet -a --reads-per-batch 12 -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 @@ -6630,57 +6648,57 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 4 --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 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 --debug --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --trim3 16 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 1 -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 --debug -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" Qseq multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Qseq multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 1 --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 Qseq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Qseq paired 1 (fw:1, sam:1) @@ -6688,10 +6706,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz +./bowtie2 --debug --quiet -a --reads-per-batch 5 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -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 @@ -6700,10 +6718,10 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz +./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" MachName_RunNum_Lane_Tile_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) @@ -6711,29 +6729,29 @@ >0 GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 23 24 2M1I40M * 0 0 ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:42 YT:Z:UU Left-align deletion (fw:1, sam:1) References: >0 GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC -./bowtie2 --debug --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 19 40 6M1D39M * 0 0 ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^A39 YT:Z:UU Left-align insertion with mismatch at LHS (fw:1, sam:1) References: >0 GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet --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:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet --reads-per-batch 16 -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: @@ -6751,10 +6769,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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) @@ -6762,10 +6780,10 @@ >0 TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --fr --quiet --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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) @@ -6773,10 +6791,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --fr --quiet --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:290 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 99 0 3 1 38M = 80 119 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 80 1 42M = 3 -119 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) @@ -6784,154 +6802,154 @@ >0 CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -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 --debug --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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^A0C39 YT:Z:UU MD:Z 2 (fw:1, sam:1) References: >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU MD:Z 2 (fw:0, sam:1) References: >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./bowtie2 --debug --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU MD:Z 3 (fw:1, sam:1) References: >0 CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-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 --debug --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-12 XN:i:3 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^NN0N39 YT:Z:UU MD:Z 4 (fw:0, sam:1) References: >0 CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./bowtie2 --debug --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:-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 --debug --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 +./bowtie2 --debug --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 --debug --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 --debug --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU r0 272 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU Local alignment 4 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU r0 256 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU Local alignment 4 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU r0 272 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU Alignment order -k (fw:1, sam:1) @@ -6939,10 +6957,10 @@ >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -6951,10 +6969,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --debug --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -6963,10 +6981,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --debug --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --min-score C,-24,0 -L 4 --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:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -6975,10 +6993,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --debug --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -6988,10 +7006,10 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 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 r0 355 0 3 255 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP @@ -7022,10 +7040,10 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --debug --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 83 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 163 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 339 0 68 255 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP @@ -7071,11 +7089,11 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --debug --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 68 1 19M = 3 -84 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 163 0 3 1 19M = 68 84 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 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 @@ -7087,143 +7105,143 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; no args (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 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 --debug --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 +./bowtie2 --debug --ff --quiet -M 1 --no-discordant --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --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 (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 +./bowtie2 --debug --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 +./bowtie2 --debug --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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-dovetail (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 --debug --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 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 --debug --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-overlap (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 --debug --no-overlap --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -7241,33 +7259,33 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 --debug --ff --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 --debug --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 --debug --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 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 --debug --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 +./bowtie2 --debug --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP Overlapping; --no-dovetail (fw:0, sam:1) @@ -7285,22 +7303,22 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --no-contain --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --no-contain --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP Overlapping; --no-contain (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 --debug --no-contain --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP Overlapping; --no-overlap (fw:1, sam:1) @@ -7318,11 +7336,11 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -7330,273 +7348,273 @@ >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -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 --debug --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 14 -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 --debug --ignore-quals --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 --debug --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 2 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 --debug --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 4 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --debug --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --ignore-quals --rdg 1,2 --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 --debug --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 5 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --debug --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-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 --debug --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 --debug --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Q XS:i 1a (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,3 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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 --debug -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 --debug -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,6 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug -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 --debug -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 --debug -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 3,3 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a I --mp 3,3 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug -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 --debug -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 --debug -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 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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 --debug -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 --debug --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 --debug --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --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 +./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --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 --debug --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1b --ignore-quals (fw:0, sam:1) References: @@ -7622,51 +7640,51 @@ References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c --ignore-quals (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --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 --debug --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU (fw:1, sam:1) References: >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 73 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP (fw:0, sam:1) References: >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT -./bowtie2 --debug --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 --debug --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 137 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP r0 69 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP (fw:1, sam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bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 217 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT -./bowtie2 --debug --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -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 --debug --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 1 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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 --debug --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU XS:i 2 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --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 --debug --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACGAACAA IIIIIIII YT:Z:UU XS:i 3a (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3b (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3c (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3c (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 --debug --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4b (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT -./bowtie2 --debug --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 --debug --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 --debug --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 +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 --debug --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --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:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5b (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA -./bowtie2 --debug --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU BWA-SW-like 1 (fw:1, sam:1) References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --bwa-sw-like --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU BWA-SW-like 1 (fw:0, sam:1) References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA -./bowtie2 --debug --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 1 -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 --debug --bwa-sw-like -L 18 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU BWA-SW-like 2 (fw:0, sam:1) References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA -./bowtie2 --debug --bwa-sw-like -L 18 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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: @@ -7983,80 +8001,80 @@ References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --debug --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 --debug --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 24M = 4 24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP r0 131 0 4 255 24M = 4 -24 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:-6 YT:Z:CP SAM paired-end where both alignments start at the same offset (rf case) (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --debug --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 --debug --rf --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 --debug --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 --debug --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP r0 147 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP SAM paired-end where both mates align 2 (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --debug --rf --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --rf --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP r0 163 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP SAM paired-end where both mates align 3 (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --debug --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP r0 131 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP SAM paired-end where mate #1 aligns but mate #2 doesn't (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --debug --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 --debug --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug --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 --debug --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP SAM paired-end where both mates align, but discordantly (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --debug --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 --debug --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -8066,11 +8084,11 @@ >1 GCTCGGAATTCGTGCTCCGNCCCGTACGGTT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --policy "NP=Q\;RDG=46.3220993654702\;RFG=41.3796024365659\;MIN=L,5.57015383125426,-3.28597145122829\;NCEIL=L,0.263054599454459,0.130843661549367\;SEED=1\;SEEDLEN=29\;IVAL=L,0.0169183264663712,3.75762168662522" --overhang --trim5 6 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 @SQ SN:1 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NP=Q;RDG=46.3220993654702;RFG=41.3796024365659;MIN=L,5.57015383125426,-3.28597145122829;NCEIL=L,0.263054599454459,0.130843661549367;SEED=1;SEEDLEN=29;IVAL=L,0.0169183264663712,3.75762168662522 --overhang --trim5 6 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACCCCTCCCTTGTCGGCTCCCACCCATCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGTCGTCACTCCCCGTTTGCGTCATGCCCCTCACCCTCCCTTTGTCGGCTCGCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCTCTCGGGGTCTTCACGCCCCGCTTGCTTCATGCCCCTCACTCGCACCCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UU matchesRef regression 4 (fw:0, sam:1) References: @@ -8089,19 +8107,19 @@ >0 GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU matchesRef regression 3 (fw:0, sam:1) References: >0 GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC -./bowtie2 --debug --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --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:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 2 -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: @@ -8110,11 +8128,11 @@ >1 CCTTGTTNTTAATGCTGCCTGGTTTNG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --policy "RDG=2.02030755427021,2.81949533273331\;MIN=L,-6.52134769703939,-3.39889659588514\;IVAL=L,0.127835912101927" --overhang --trim5 5 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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 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:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 9 -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) @@ -8123,11 +8141,11 @@ GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG >1 CCTTGTTNTTAATGCTGCCTGGTTTNG -./bowtie2 --debug --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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 89 0 1 255 29S23M = 1 0 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YT:Z:UP r0 165 0 1 0 * = 1 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP matchesRef regression 1 (fw:1, sam:1) @@ -8144,10 +8162,10 @@ References: >0 AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC -./bowtie2 --debug --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --overhang --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:61 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 12 255 50M10S * 0 0 AAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTACTGGTCTGGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:9 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU Discordant with different chromosomes (fw:1, sam:1) References: @@ -8156,11 +8174,11 @@ >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -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 --debug -I 0 -X 35 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 65 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 65 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP @@ -8171,11 +8189,11 @@ TTTATAAAAATATTTCCCCCCCC >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC -./bowtie2 --debug -I 0 -X 35 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --debug -I 0 -X 35 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 113 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 113 1 7 255 10M 0 4 0 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP @@ -8185,28 +8203,28 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 --debug -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug -s 1 --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 +./bowtie2 --debug -s 1 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r1 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) @@ -8223,34 +8241,34 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -s 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug -s 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug -s 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -s 2 --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 +./bowtie2 --debug -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 2 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:1, sam:1) References: >0 @@ -8264,151 +8282,151 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -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 +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug -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 --debug -s 1 --trim3 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 12 -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 --debug -s 1 --trim3 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --trim3 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug -s 1 --trim5 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug -s 1 --trim5 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --trim5 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug -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 --debug -s 1 --trim5 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 --debug --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU (fw:0, sam:1) References: >0 TGC -./bowtie2 --debug --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 --debug --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --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 --debug --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --debug --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --debug --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --debug --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 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 --debug --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --debug --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --debug --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r0 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 @@ -8416,10 +8434,10 @@ References: >0 TTGTTCGT -./bowtie2 --debug --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" 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 @@ -8427,10 +8445,10 @@ References: >0 TTGTTCGT -./bowtie2 --debug --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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 @@ -8439,10 +8457,10 @@ References: >0 TTGTTCGT -./bowtie2 --debug --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 --debug --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r2 4 * 0 0 * * 0 0 TACGAAC IIIIIII YT:Z:UU @@ -8451,10 +8469,10 @@ References: >0 TTGTTCGT -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: @@ -8469,73 +8487,73 @@ References: >0 TTGTTCGT -./bowtie2 --debug --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --overhang --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 13 -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 --debug --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU P.M.58.G.b Unpaired -M 5 w/ 8 hits global, but mate #1 has just 1 (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -X 1000 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 724 1 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.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 --debug -X 1000 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug -X 1000 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 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 --debug -X 1000 --local --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug -X 1000 --local --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 724 739 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 724 1 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.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 --debug -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 --debug -X 1000 --local --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 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 --debug -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 +./bowtie2 --debug -X 1000 --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --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" r0 99 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 355 0 13 255 33M = 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 @@ -8550,10 +8568,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --debug -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 +./bowtie2 --debug -X 1000 --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP @@ -8568,10 +8586,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --debug -X 1000 --local --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug -X 1000 --local --fr --quiet -k 5 --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:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 355 0 13 255 33M = 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 @@ -8586,10 +8604,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --debug -X 1000 --local --fr --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 339 0 724 255 28M = 13 -739 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP @@ -8605,64 +8623,64 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -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 +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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 --debug -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 +./bowtie2 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -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 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.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --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 --debug --local -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --local -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --local -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug -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 --debug -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.k.2.G. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug -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 +./bowtie2 --debug -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -8679,10 +8697,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) @@ -8700,33 +8718,33 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --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 --debug --fr --quiet -M 1 -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 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 --debug --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 --debug --fr --quiet -M 1 --local -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.M.2.L. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --fr --quiet -M 1 --local -X 150 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -M 1 --local -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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) @@ -8734,84 +8752,84 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --fr --quiet -k 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 --debug --fr --quiet -k 1 -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -k 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug --fr --quiet -k 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --fr --quiet -k 1 -X 150 --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:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --fr --quiet -k 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 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 --debug --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 +./bowtie2 --debug --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 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 --debug -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 --debug -X 150 --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug -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 +./bowtie2 --debug -X 150 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug -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 --debug -X 150 --local --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --local --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 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 --debug -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 --debug -X 150 --local --fr --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) @@ -8819,22 +8837,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -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 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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.58.G. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA -./bowtie2 --debug -X 150 --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 --debug -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 553 1 28M = 487 -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 0 487 1 33M = 553 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) @@ -8842,22 +8860,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --local -X 150 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 961 1 33M = 1027 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 1027 1 28M = 961 -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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 1264 1 28M = 1198 -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 1198 1 33M = 1264 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) @@ -8865,127 +8883,127 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -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 --debug --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 3 -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 --debug --local --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 13 44 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.L. Unpaired -M w/ 1 hit local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --debug --local --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -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 --debug --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -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 --debug --local --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 5 -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 --debug --local --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --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: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 --debug --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --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.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 1 --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.2.G. Unpaired -k 1 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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: @@ -9009,89 +9027,89 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 --debug --quiet -M 2 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 --debug --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -M 2 --local --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 --debug --quiet -M 2 --local --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 --debug --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 272 0 49 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --quiet -k 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU 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 --debug --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --quiet -k 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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) @@ -9109,11 +9127,11 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug -X 150 --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug -X 150 --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) References: @@ -9129,20 +9147,20 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --local --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -k 5 --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:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 5 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 5 --reads-per-batch 5 -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 @@ -9152,10 +9170,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 5 --reads-per-batch 16 -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 @@ -9165,10 +9183,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --local --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --quiet -k 5 --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:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 304 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 256 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 256 0 177 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU @@ -9178,10 +9196,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --local --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --local --quiet -k 5 --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:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 10 -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 @@ -9192,49 +9210,49 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -L 6 -i C,1,0 --policy "MMP=C27\;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 --debug -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug -L 6 -i C,1,0 --policy "MMP=C27\;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 --debug -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 12 -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 --debug -L 6 -i C,1,0 --policy "MMP=C28\;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 +./bowtie2 --debug -L 6 -i C,1,0 --policy "MMP=C28\;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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 3 -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 --debug -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 --debug -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 4 -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 --debug --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 +./bowtie2 --debug --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 0 0 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 @@ -9255,10 +9273,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --debug --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 +./bowtie2 --debug --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 16 0 14 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -9280,196 +9298,196 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 13 -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 --debug --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 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU Gap penalties 2 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 15 -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 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU Gap penalties 3 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU Gap penalties 3 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 10 -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 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU Gap penalties 5 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU Gap penalties 5 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU Gap penalties 6 (fw:1, sam:1) References: >0 ATTGTTCGTTTGTTCGTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=19,10\;RFG=18,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 6M1D5M1I6M * 0 0 ATTGTTGTTTGATTCGTA IIIIIIIIIIIIIIIIII AS:i:-57 XN:i:0 XM:i:0 XO:i:2 XG:i:2 NM:i:2 MD:Z:6^C11 YT:Z:UU Gap penalties 7 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=16,10\;RFG=16,10\;MIN=L,-3,-3" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU N filtering 1 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAACTATCGCTCTA -./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU N filtering 2 (fw:1, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 2 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:1, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA -./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 --debug --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 4 (fw:0, sam:1) References: @@ -9485,123 +9503,123 @@ >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU N filtering 5 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --debug --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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: >0 GAGACTTTNTACGCATCGAANTATCGCTCTA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 6 (fw:0, sam:1) References: >0 GAGACTTTNTACGCATCGAANTATCGCTCTA -./bowtie2 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTTTGTTCGTTTG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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 --debug --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 --debug --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU (fw:1, sam:1) References: >0 ACNCA ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --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:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 --debug --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 --debug --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:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 2M * 0 0 AC II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (1) (fw:0, sam:1) References: >0 ACNCA -./bowtie2 --debug --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 --debug --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:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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 --debug --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 +./bowtie2 --debug --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 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 @@ -9610,10 +9628,10 @@ References: >0 ACNCANNNNNNNNCGNNNNNNNNCG -./bowtie2 --debug --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 --debug --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 @@ -9623,10 +9641,10 @@ >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -9637,10 +9655,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --debug --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 +./bowtie2 --debug --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:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -9651,10 +9669,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 @@ -9665,10 +9683,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --debug --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 --debug --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 14 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 272 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -9680,10 +9698,10 @@ >0 TTGTTYGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 0 0 1 255 8M * 0 0 TTGTTGGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU r1 0 0 1 255 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU (fw:1, sam:1) @@ -9691,19 +9709,19 @@ >0 ATAACCTTCG ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU (fw:0, sam:1) References: >0 ATAACCTTCG -./bowtie2 --debug --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 +./bowtie2 --debug --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU (fw:1, sam:1) References: @@ -9719,20 +9737,20 @@ References: >0 ATATGCCCCATGCCCCCCTCCG -./bowtie2 --debug --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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:22 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU Simple paired-end 13 (fw:1, sam:1) References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -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 +./bowtie2 --debug -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 65 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP @@ -9753,10 +9771,10 @@ References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC -./bowtie2 --debug -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 +./bowtie2 --debug -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,.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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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,.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 @@ -9778,10 +9796,10 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -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 --debug -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 67 0 4 255 10M = 28 34 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP @@ -9790,10 +9808,10 @@ References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC -./bowtie2 --debug -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --debug -I 0 -X 36 --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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,.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 @@ -9803,20 +9821,20 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -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 +./bowtie2 --debug -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug -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 --debug -I 0 -X 36 --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:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 -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) @@ -9834,10 +9852,10 @@ References: >0 TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC -./bowtie2 --debug -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 +./bowtie2 --debug -I 28 -X 80 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 113 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP Simple paired-end 9 (fw:1, sam:1) @@ -9856,11 +9874,11 @@ References: >0 CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC -./bowtie2 --debug -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -9868,10 +9886,10 @@ >0 CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -I 0 -X 80 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug -I 0 -X 80 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 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 @@ -9882,10 +9900,10 @@ References: >0 CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC -./bowtie2 --debug -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 --debug -I 0 -X 80 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 163 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 339 0 60 255 10M = 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 @@ -9897,10 +9915,10 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -I 0 -X 50 --nofw --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 --debug -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --nofw --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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) @@ -9908,20 +9926,20 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -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 +./bowtie2 --debug -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 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 --debug -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 +./bowtie2 --debug -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -9929,20 +9947,20 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 131 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Simple paired-end 1 (fw:0, sam:1) References: >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC -./bowtie2 --debug -I 0 -X 50 --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 --debug -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 179 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP (fw:1, sam:1) @@ -9950,10 +9968,10 @@ >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --debug --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 @@ -9974,10 +9992,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 16 0 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 @@ -9999,104 +10017,104 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT ./bowtie2-build --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --policy SEED=0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy SEED=0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --policy SEED=0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy SEED=0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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 --debug --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --policy "SEED=0\;SEEDLEN=2\;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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 2 -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 @@ -10107,10 +10125,10 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 --debug --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-s-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -10122,20 +10140,20 @@ >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 14 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU seq1_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,9 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU seq2_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU seq2_9 0 0 10 255 10M * 0 0 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU @@ -10143,38 +10161,38 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,9 -u 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU FASTA-continuous 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 1 -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 9 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 7 -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 9 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --large-index -F 10,1 --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:12 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -F 10,1 --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 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 @@ -10187,11 +10205,11 @@ ./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 9 -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:15 @SQ SN:1 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -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: @@ -10206,56 +10224,56 @@ 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 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:15 @SQ SN:1 LN:15 @SQ SN:2 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 0 0 2 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Should account for stretch of Ns at beginning (fw:1, sam:1) References: >0 NNNNNNNNNNNNNNNAGCATCGATCAGTATCTGA ./bowtie2-build --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 11 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -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 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP +./bowtie2 --large-index --quiet -a --reads-per-batch 3 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG ABCDEDGHIJKLMNOP AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO +./bowtie2 --large-index --quiet -a --reads-per-batch 2 -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 @@ -10264,7 +10282,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ +./bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ Error: Read 0 has more quality values than read characters. terminate called after throwing an instance of 'int' Aborted @@ -10273,37 +10291,37 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim-to 5:12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 5:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 7 255 12M * 0 0 GATCAGTATCTG IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: trim from 3'-end (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim-to 3:12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 3:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: trim from 3'-end (default) (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim-to 12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: invalid position (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim-to 4:12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 4:12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: trim position must be either 3 or 5 Bowtie 2 version 2.5.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -10456,13 +10474,13 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 9 -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 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII --trim-to: the number bases to trim must be at least 0 Bowtie 2 version 2.5.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -10615,67 +10633,67 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 2 -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 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Cline 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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: >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 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" Cline multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --large-index --quiet -a --reads-per-batch 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Cline multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 5 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 5 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Cline paired 1 (fw:1, sam:1) @@ -10683,10 +10701,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII +./bowtie2 --large-index --quiet -a --reads-per-batch 16 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -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 @@ -10695,30 +10713,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 4 -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 16 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Cline paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -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 3 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII +./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 6 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 6 -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) @@ -10726,34 +10744,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 4 -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 @@ -10762,7 +10780,7 @@ 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 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 @@ -10771,7 +10789,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 2 -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 @@ -10780,10 +10798,10 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 5 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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: @@ -10798,37 +10816,37 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -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 16 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --large-index -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq paired 1 (fw:1, sam:1) @@ -10836,10 +10854,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --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 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/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 @@ -10848,20 +10866,20 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Fastq paired 4 (fw:1, sam:1) @@ -10879,34 +10897,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 12 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 15M * 0 0 CATCGATCAGTATCT IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 8 -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 @@ -10915,7 +10933,7 @@ 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 4 -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 @@ -10924,85 +10942,85 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Fasta 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --trim3 16 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Fasta 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 15 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 1 (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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta paired 1 (fw:1, sam:1) @@ -11010,10 +11028,10 @@ >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 -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP @@ -11022,30 +11040,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP Fasta paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 2 -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 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Fasta paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 10 -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 1 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 1 -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) @@ -11053,82 +11071,82 @@ >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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Raw 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Raw 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -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 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 4 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --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 multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --large-index -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Raw paired 1 (fw:1, sam:1) @@ -11136,10 +11154,10 @@ >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 -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 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 @@ -11148,30 +11166,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --large-index -s 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -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 10 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 --large-index -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 +./bowtie2 --large-index -3 7 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 9 -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) @@ -11179,34 +11197,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted @@ -11215,7 +11233,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 1 -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 @@ -11224,55 +11242,55 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 3 -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 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Tabbed 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" Tabbed multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --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 multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Tabbed paired 1 (fw:1, sam:1) @@ -11280,10 +11298,10 @@ >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 --tab5 .simple_tests.tab.gz +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --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 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 @@ -11292,30 +11310,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Tabbed paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --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 Tabbed paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --large-index -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --large-index -3 7 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 9 -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) @@ -11323,37 +11341,37 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -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 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 10 -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 @@ -11362,57 +11380,57 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --trim3 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index -s 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" Qseq multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_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 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --large-index -u 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -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 4 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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) @@ -11420,10 +11438,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --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 +./bowtie2 --large-index --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" 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 @@ -11443,39 +11461,39 @@ >0 GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet --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:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 23 24 2M1I40M * 0 0 ACAAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:42 YT:Z:UU Left-align deletion (fw:1, sam:1) References: >0 GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC -./bowtie2 --large-index --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet --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:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 15 -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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 5 24 20M1D45M * 0 0 TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20^A0A44 YT:Z:UU Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) References: >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1192 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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) @@ -11483,10 +11501,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet --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 --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:1028 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -11494,10 +11512,10 @@ >0 TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG ./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 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:250 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -11516,124 +11534,124 @@ >0 CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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^A0C39 YT:Z:UU MD:Z 1 (fw:0, sam:1) References: >0 CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 8 -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 4 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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: >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./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 2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU MD:Z 3 (fw:1, sam:1) References: >0 CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU MD:Z 3 (fw:0, sam:1) References: >0 CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./bowtie2 --large-index --quiet -a --reads-per-batch 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 --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 10 -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 12 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU Local alignment 1 (fw:0, sam:1) References: >0 TTGT -./bowtie2 --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 6 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU Local alignment 2 (fw:1, sam:1) References: >0 TTGA ./bowtie2-build --large-index --quiet .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 13 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -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 13 -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 4 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 4 -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 5 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 38 13M * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:26 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU r0 256 0 9 255 8M5S * 0 0 TTGTTCGTTTGTT IIIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU Local alignment 3 (fw:0, sam:1) @@ -11660,10 +11678,10 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 14 -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) @@ -11671,10 +11689,10 @@ >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 9 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -11683,10 +11701,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 5 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 @@ -11695,10 +11713,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 256 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 256 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -11707,10 +11725,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 9 -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 16 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 16 -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 @@ -11720,10 +11738,10 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 99 0 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 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 @@ -11754,10 +11772,10 @@ 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 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 83 0 169 1 19M = 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 r0 339 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP @@ -11819,33 +11837,33 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; no args (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 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 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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) @@ -11863,66 +11881,66 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 14 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 9 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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) @@ -11940,121 +11958,121 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./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 +./bowtie2 --large-index --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" 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 8 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-overlap --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-overlap (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 4 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 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 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP Overlapping; --no-contain (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 8 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP r0 179 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP Overlapping; --no-overlap (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 6 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-overlap --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 6 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --no-overlap --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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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) @@ -12062,263 +12080,263 @@ >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 12 -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:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 12 -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:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU Scoring params 2 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG ./bowtie2-build --large-index --quiet .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 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ignore-quals --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 9 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 5 -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 3 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 9 -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 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 15 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-30 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 5 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 5 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-40 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 6 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 6 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Q XS:i 1a (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA ./bowtie2-build --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,3 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,6 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --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 +./bowtie2 --large-index -L 6 --mp 6,3 --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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a I --mp 3,3 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" 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 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 4 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 --mp 6,3 --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:-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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a --ignore-quals (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 11 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 11 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-4 XS:i:-4 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1b --ignore-quals (fw:1, sam:1) References: @@ -12334,71 +12352,71 @@ 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT 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 8 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c --ignore-quals (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c --ignore-quals (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU (fw:1, sam:1) References: >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 73 0 2 255 27M = 2 0 ATCGACTGAGACTCGTACGACAATTAC IIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:27 YT:Z:UP r0 133 0 2 0 * = 2 0 TAGGTTTCGCGCGAAACGCTGGTGAT IIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP (fw:0, sam:1) References: >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 10 -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 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:68 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --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 7 -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 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:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 13 -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 6 -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 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:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 14 -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 2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 9 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -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 8 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU XS:i 1 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU XS:i 2 (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU XS:i 2 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 9 -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: @@ -12517,198 +12535,198 @@ References: >0 TTGTTCGATTGTTCGT -./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 +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 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 5 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3b (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 11 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3c (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3c (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 12 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 6 -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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4b (fw:1, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT -./bowtie2 --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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4b (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT -./bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5a (fw:1, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA ./bowtie2-build --large-index --quiet .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 12 -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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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 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:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5b (fw:1, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA -./bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 9 -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 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5b (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA -./bowtie2 --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 14 -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 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:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like --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:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 7 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:56 YT:Z:UU BWA-SW-like 2 (fw:1, sam:1) References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA -./bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --bwa-sw-like -L 18 --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:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 4 255 56M * 0 0 TAGATTCCACTACGCTAACCATCGAGTTCTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:48 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:26A0A28 YT:Z:UU BWA-SW-like 3 (fw:1, sam:1) References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA -./bowtie2 --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 8 -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 2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -12725,70 +12743,70 @@ References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --large-index --rf --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 --rf --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --rf --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 4 255 24M = 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 10 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGTGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:21C2 YS:i:0 YT:Z:CP r0 147 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:-6 YT:Z:CP SAM paired-end where both mates align 2 (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --large-index --rf --quiet -a --reads-per-batch 14 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --rf --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 11 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 4 255 24M = 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 10 -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 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 4 255 24M = 36 53 CTATCTACGCTTCGGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:24 YS:i:0 YT:Z:DP r0 129 0 36 255 21M = 4 -53 ACGACCGGGTGTGTGACAATC IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP matchesRef regression 4 (fw:1, sam:1) @@ -12798,11 +12816,11 @@ >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 9 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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: @@ -12810,30 +12828,30 @@ 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 16 -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 3 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -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 1 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 10 255 38M * 0 0 CCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:38 YT:Z:UU matchesRef regression 3 (fw:0, sam:1) References: >0 GAAGNTTTTCCAATATTTTTAATTTCCTCTATTTTTCTCTCGTCTTGNTCTAC -./bowtie2 --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 12 -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 8 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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: @@ -12842,11 +12860,11 @@ >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 9 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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) @@ -12855,11 +12873,11 @@ 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 14 -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 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 89 0 1 255 29S23M = 1 0 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YT:Z:UP r0 165 0 1 0 * = 1 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP matchesRef regression 1 (fw:1, sam:1) @@ -12876,10 +12894,10 @@ References: >0 AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC -./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:61 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -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: @@ -12888,11 +12906,11 @@ >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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 @@ -12903,11 +12921,11 @@ TTTATAAAAATATTTCCCCCCCC >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC -./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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.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 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 -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 @@ -12917,64 +12935,64 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 14 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --fr --quiet -a --reads-per-batch 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 -s 1 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r1 99 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r1 147 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" r1 83 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r1 163 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index -s 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --large-index -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:0, sam:1) References: >0 @@ -12987,111 +13005,111 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --large-index -s 1 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r1 16 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 8 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --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 +./bowtie2 --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 6 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 9 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 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: @@ -13107,40 +13125,40 @@ References: >0 TTGTTCGT -./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 0 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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,.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 @@ -13148,10 +13166,10 @@ 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 7 -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 16 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r0 16 0 2 255 7M * 0 0 TGTTCGT IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU r1 16 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU r2 16 0 1 255 1S6M * 0 0 ATTGTTC IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU @@ -13159,10 +13177,10 @@ References: >0 TTGTTCGT -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 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 +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.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 @@ -13171,10 +13189,10 @@ References: >0 TTGTTCGT -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 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 +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.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 @@ -13183,91 +13201,91 @@ 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 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,2,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --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 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 7 -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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" r0 99 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.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 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:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 4 -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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.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 3 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --local --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 0 961 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 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 355 0 13 255 33M = 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 @@ -13282,10 +13300,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./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 +./bowtie2 --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 961 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 r0 339 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP @@ -13300,10 +13318,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 = 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 @@ -13318,10 +13336,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 961 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 r0 339 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP @@ -13337,44 +13355,44 @@ >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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 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 5 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 1 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 316 1 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.M.22.L. Paired -M 2 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 3 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -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:2.5.0 CL:"/build/bowtie2-2.5.0/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) @@ -13391,74 +13409,74 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index -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 +./bowtie2 --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 255 33M = 316 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 316 255 28M = 250 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.k.2.L. Paired -k 1 w/ 2 paired hit, 2 unpaired hits each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 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 -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.M.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 1 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 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 --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 11 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 --large-index --fr --quiet -M 1 --local -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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) @@ -13466,84 +13484,84 @@ >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 6 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.k.1.G. Paired -k w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 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 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:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" 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 11 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 2 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 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 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 44 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 79 44 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.M.1.L. Paired -M w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 2 -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 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" 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) @@ -13551,22 +13569,22 @@ >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 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:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 487 1 33M = 553 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 0 553 1 28M = 487 -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 5 -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 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:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 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) @@ -13574,22 +13592,22 @@ >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 8 -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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC -./bowtie2 --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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 83 0 1264 1 28M = 1198 -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 1198 1 33M = 1264 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) @@ -13597,203 +13615,203 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA ./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:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.G. Unpaired -M w/ 1 hit global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 7 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --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:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 3 -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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --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: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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --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:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --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:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -M 2 --local --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -M 2 --local --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 2 --local --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.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 2 --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:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 2 --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: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) @@ -13810,20 +13828,20 @@ 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.G. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) @@ -13831,50 +13849,50 @@ >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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index -X 150 --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 134 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 5 --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:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 14 -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 @@ -13884,10 +13902,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 5 --reads-per-batch 2 -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 @@ -13897,10 +13915,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --large-index --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --local --quiet -k 5 --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:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 14 -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 @@ -13924,49 +13942,49 @@ >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 15 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 16 -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 5 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 12 -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 6 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCAT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 0 0 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 @@ -13987,10 +14005,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --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 +./bowtie2 --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 @@ -14012,110 +14030,110 @@ >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 10 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU Gap penalties 1 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 5 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU Gap penalties 2 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU Gap penalties 3 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 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 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -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 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=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU Gap penalties 5 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --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 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=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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 9 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 9 -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 4 -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 11 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 11 -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: @@ -14131,199 +14149,199 @@ 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 2 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=16,10;RFG=16,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACGAATCAAACAACAA IIIIIIIIIIIIIIII YT:Z:UU N filtering 1 (fw:1, sam:1) References: >0 GAGACTTTATACGCATCGAACTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU N filtering 1 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAACTATCGCTCTA -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU N filtering 2 (fw:1, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 2 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:1, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA ./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 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 4 (fw:1, sam:1) References: >0 GAGACTTTNTACGCATCGAACTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 12 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" r0 0 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU N filtering 5 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU N filtering 6 (fw:1, sam:1) References: >0 GAGACTTTNTACGCATCGAANTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 6 (fw:0, sam:1) References: >0 GAGACTTTNTACGCATCGAANTATCGCTCTA -./bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTTTGTTCGTTTG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 9M1I4M * 0 0 TTTTGTTCGATTTG IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU (fw:0, sam:1) References: >0 TTTTGTTCGTTTG -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -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 2 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 13 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 16 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 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 11 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 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 13 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 15 -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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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: @@ -14342,10 +14360,10 @@ References: >0 ACNCANNNNNNNNCGNNNNNNNNCG -./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 +./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 24 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -14355,10 +14373,10 @@ >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 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 @@ -14369,10 +14387,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/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 @@ -14383,10 +14401,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -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:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 @@ -14397,10 +14415,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 10 -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 9 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 @@ -14412,10 +14430,10 @@ >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 15 -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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 10 -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) @@ -14423,48 +14441,48 @@ >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 13 -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 12 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 12 -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 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 4 -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 15 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=5,5;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 9M3D10M * 0 0 ATATGCCCCCCCCCCTCCG IIIIIIIIIIIIIIIIIII AS:i:-20 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:9^ATG10 YT:Z:UU (fw:1, sam:1) References: >0 ATATGCCCCATGCCCCCCTCCG -./bowtie2 --large-index --quiet -a --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=5,5\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 8 -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 13 -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:2.5.0 CL:"/build/bowtie2-2.5.0/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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 13 -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 15 -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 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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 @@ -14485,10 +14503,10 @@ References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC -./bowtie2 --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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:2.5.0 CL:"/build/bowtie2-2.5.0/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 @@ -14510,10 +14528,10 @@ >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 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 -I 0 -X 36 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 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 @@ -14522,10 +14540,10 @@ References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC -./bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 @@ -14535,20 +14553,20 @@ >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 16 -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 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 0 31 255 10M = 4 -37 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP Simple paired-end 11 (fw:0, sam:1) References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC -./bowtie2 --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 16 -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 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:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -14556,20 +14574,20 @@ >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 13 -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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP Simple paired-end 10 (fw:0, sam:1) References: >0 TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC -./bowtie2 --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 13 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 28 -X 80 --ff --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:2.5.0 CL:"/build/bowtie2-2.5.0/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) @@ -14577,22 +14595,22 @@ >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 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:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Simple paired-end 9 (fw:0, sam:1) References: >0 CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC -./bowtie2 --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -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 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:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -14600,10 +14618,10 @@ >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 4 -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 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:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 4 1 10M = 60 66 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 60 1 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 355 0 38 255 10M = 60 32 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP @@ -14614,10 +14632,10 @@ 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 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:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 80 --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 83 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 163 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 339 0 60 255 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP @@ -14629,10 +14647,10 @@ >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 7 -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 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:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --nofw --ff --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --nofw --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 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) @@ -14640,20 +14658,20 @@ >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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 16 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP Simple paired-end 1 (fw:1, sam:1) @@ -14661,20 +14679,20 @@ >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 13 -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 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 2 -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 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 -I 0 -X 50 --ff --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:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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) @@ -14682,10 +14700,10 @@ >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --large-index --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 --quiet -k 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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" 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 @@ -14706,10 +14724,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --large-index --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --large-index --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --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" 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 @@ -14731,104 +14749,104 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 13 -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:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -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 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,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 3 255 6M1S * 0 0 GTTCGTA IIIIIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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" 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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy SEED=0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --large-index --policy SEED=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:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --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 --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --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:2.5.0 CL:"/build/bowtie2-2.5.0/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" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/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 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 11 -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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 256 0 1 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 256 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU @@ -14839,10 +14857,10 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --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=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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 2 -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 @@ -14854,20 +14872,20 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -F 10,9 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug --large-index -F 10,9 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU seq1_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 --debug --large-index -F 10,9 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug --large-index -F 10,9 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,9 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp .simple_tests.gz" seq1_0 0 0 1 255 10M * 0 0 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YT:Z:UU 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 @@ -14875,38 +14893,38 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug --large-index -F 10,9 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,9 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,9 -u 1 --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 FASTA-continuous 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -F 10,9 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug --large-index -F 10,9 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,9 -s 1 --quiet -a --reads-per-batch 13 -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 --debug --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug --large-index -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,9 -u 1 -s 1 --quiet -a --reads-per-batch 7 -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 --debug --large-index -F 10,1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz +./bowtie2 --debug --large-index -F 10,1 --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:12 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp .simple_tests.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -F 10,1 --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_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 @@ -14919,11 +14937,11 @@ ./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 --debug --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -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: @@ -14938,12 +14956,12 @@ Warning: Encountered reference sequence with only gaps Warning: Encountered reference sequence with only gaps Warning: Encountered reference sequence with only gaps -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 10 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -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: @@ -14960,34 +14978,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG +./bowtie2 --debug --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:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 12 -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 --debug --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Cline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 7 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOP" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -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 --debug --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNO +./bowtie2 --debug --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 @@ -14996,7 +15014,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -c CATCGATCAGTATCTG:ABCDEDGHIJKLMNOPQ +./bowtie2 --debug --large-index --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 @@ -15005,37 +15023,37 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim-to 5:12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --large-index --trim-to 5:12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim-to 5:12 --quiet -a --reads-per-batch 15 -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 --debug --large-index --trim-to 3:12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --large-index --trim-to 3:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim-to 3:12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU trim-to: trim from 3'-end (default) (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim-to 12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --large-index --trim-to 12 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim-to 12 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim-to 12 --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 trim-to: invalid position (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim-to 4:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --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 2.5.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -15188,13 +15206,13 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim-to 4:12 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --trim-to 5:-12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --large-index --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 2.5.0 by Ben Langmead (langmea@cs.jhu.edu, www.cs.jhu.edu/~langmea) @@ -15347,67 +15365,67 @@ --version print version information and quit -h/--help print this usage message Error: Encountered internal Bowtie 2 exception (#1) -Command: /build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim-to 5:-12 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +Command: /build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --large-index --trim3 4 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Cline 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim5 16 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --large-index --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Cline 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII +./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII" Cline multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Cline multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -c CATCGATCAGTATCTG:IIIIIIIIIIIIIIII,ATCGATCAGTATCTG:IIIIIIIIIIIIIII +./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 3 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -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 --debug --large-index -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG +./bowtie2 --debug --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c CATCGATCAGTATCTG,ATCGATCAGTATCTG" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Cline paired 1 (fw:1, sam:1) @@ -15415,10 +15433,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA -2 TCAGTTTTTGA,AGCATCGATC:IIIIIIIIII" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP @@ -15427,30 +15445,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 --debug --large-index -s 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 2 -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 --debug --large-index -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII +./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -c -1 AGCATCGATC:IIIIIIIIII,TCAGTTTTTGA:IIIIIIIIIII -2 TCAGTTTTTGA:IIIIIIIIIII,AGCATCGATC:IIIIIIIIII" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Cline paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII +./bowtie2 --debug --large-index -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -c -1 AGCATCG:IIIIIII -2 GATCAAAAACTGA:IIIIIIIIIIIII" 0 137 0 7 255 6M = 7 0 GATCAA IIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:6 YT:Z:UP 0 69 0 7 0 * = 7 0 * * YT:Z:UP YF:Z:LN Fastq 1 (fw:1, sam:1) @@ -15458,28 +15476,28 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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: @@ -15494,7 +15512,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted @@ -15503,7 +15521,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz Error: reads file does not look like a FASTQ file terminate called after throwing an instance of 'int' Aborted @@ -15512,55 +15530,55 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --large-index --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 12 -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 --debug --large-index --trim5 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --large-index --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Fastq 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.fq.gz" Fastq multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --large-index -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fastq multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz +./bowtie2 --debug --large-index -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.fq.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fastq paired 1 (fw:1, sam:1) @@ -15568,10 +15586,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP @@ -15580,30 +15598,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 163 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Fastq paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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 --debug --large-index -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz +./bowtie2 --debug --large-index -3 7 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1.fq.gz -2 .simple_tests.2.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 3 -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) @@ -15611,34 +15629,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 15M * 0 0 CATCGATCAGTATCT IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Fasta 5 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --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 @@ -15647,7 +15665,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 14 -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 @@ -15656,46 +15674,46 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --large-index --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -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 --debug --large-index --trim3 16 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --large-index --trim3 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Fasta 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --large-index -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" Fasta multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --large-index -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --large-index -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --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 multiread 3 (fw:1, sam:1) References: @@ -15711,30 +15729,30 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --large-index -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Fasta multiline 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -f .simple_tests.fa.gz +./bowtie2 --debug --large-index -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -f .simple_tests.fa.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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) @@ -15742,10 +15760,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP @@ -15754,30 +15772,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r1 83 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP r1 163 0 1 255 9M = 9 19 AGCATCGAT IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YS:i:0 YT:Z:CP Fasta paired 3 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Fasta paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -3 7 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -f -1 .simple_tests.1.fa.gz -2 .simple_tests.2.fa.gz +./bowtie2 --debug --large-index -3 7 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -3 7 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 15 -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) @@ -15785,82 +15803,82 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 Raw 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Raw 7 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --large-index --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 0 0 3 255 12M * 0 0 CATCGATCAGTA IIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU Raw 8 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim3 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --large-index --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -r .simple_tests.raw.gz" 0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Raw 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --large-index -u 1 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --large-index -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --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 multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz +./bowtie2 --debug --large-index -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -r .simple_tests.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --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 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) @@ -15868,10 +15886,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -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 @@ -15880,30 +15898,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz +./bowtie2 --debug --large-index -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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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 --debug --large-index -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 --debug --large-index -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz" 0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP 0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Raw paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --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 +./bowtie2 --debug --large-index -3 7 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -r -1 .simple_tests.1.raw.gz -2 .simple_tests.2.raw.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 10 -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) @@ -15911,34 +15929,34 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Tabbed 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 14 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz Error: Read r0 has more read characters than quality values. terminate called after throwing an instance of 'int' Aborted @@ -15947,7 +15965,7 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz Error: Read r0 has more quality values than read characters. terminate called after throwing an instance of 'int' Aborted @@ -15956,55 +15974,55 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim3 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 3 -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 --debug --large-index --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim5 16 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN Tabbed 9 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" Tabbed multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Tabbed multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --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 multiread 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index -u 2 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r1 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Tabbed paired 1 (fw:1, sam:1) @@ -16012,10 +16030,10 @@ >0 AGCATCGATCAAAAACTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP 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 @@ -16024,30 +16042,30 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -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 --debug --large-index -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" r0 99 0 1 255 10M = 9 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 147 0 9 255 11M = 1 -19 TCAAAAACTGA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP Tabbed paired 4 (fw:1, sam:1) References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz +./bowtie2 --debug --large-index -3 7 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --tab5 .simple_tests.tab.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -3 7 --quiet -a --reads-per-batch 10 -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) @@ -16055,37 +16073,37 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 3 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU Argument "MachName_RunNum_Lane_Tile_X_Y_Index" isn't numeric in int at scripts/test/simple_tests.pl line 5052. Qseq 4 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 6 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --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 @@ -16094,57 +16112,57 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --large-index --trim3 4 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 4 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 0 0 3 255 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 --debug --large-index --trim3 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --large-index --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --trim3 16 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_X_Y_Index/0 4 * 0 0 * * 0 0 * * YT:Z:UU YF:Z:LN 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 --debug --large-index -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --large-index -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" Qseq multiread 1 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU MachName_RunNum_Lane_Tile_12_15_Index/0 0 0 4 255 15M * 0 0 ATCGATCAGTATCTG IIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:15 YT:Z:UU Qseq multiread 2 (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --large-index -u 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 1 --quiet -a --reads-per-batch 12 -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 --debug --large-index -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz +./bowtie2 --debug --large-index -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -u 2 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp --qseq .simple_tests_qseq.txt.gz" MachName_RunNum_Lane_Tile_10_10_Index/0 0 0 3 255 16M * 0 0 CATCGATCAGTATCTG IIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU 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) @@ -16164,10 +16182,10 @@ References: >0 AGCATCGATCAAAAACTGA -./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz +./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp --qseq -1 .simple_tests.1_qseq.txt.gz -2 .simple_tests.2_qseq.txt.gz" MachName_RunNum_Lane_Tile_12_15_Index 83 0 9 255 11M = 1 -19 TCAAAAACTGA 57865494859 AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YS:i:0 YT:Z:CP MachName_RunNum_Lane_Tile_12_15_Index 163 0 1 255 10M = 9 19 AGCATCGATC AGGCBBGCBG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP Left-align insertion (fw:1, sam:1) @@ -16175,39 +16193,39 @@ >0 GCGATATCTACGACTGCTACGTACAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --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:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet --reads-per-batch 8 -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 --debug --large-index --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 19 40 6M1D39M * 0 0 ACGTACAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^A39 YT:Z:UU Left-align insertion with mismatch at LHS (fw:1, sam:1) References: >0 GCGATATCTACGACTGCTACGCCCAAAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGACAGC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:73 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 5 24 20M1D45M * 0 0 TATCTACGACTGCTACGCCCTAAAAAAAAAAAAGTGTTTACGTTGCTAGACTCGATCGATCTGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:20^A0A44 YT:Z:UU Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) References: >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 = 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) @@ -16215,10 +16233,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --large-index --fr --quiet --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1028 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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) @@ -16226,10 +16244,10 @@ >0 TTCACCATTTTTCTTTTCGTTAACTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTTCATCTGCAGGTGTCTGACTTCCAGCAACTGCTGGCCTGTGCCAGGGTGCAAGCTGAGCACTGGAGTGGAGTTTTCCTGTGGAGAGGAGCCATGCCTAGAG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --large-index --fr --quiet --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:250 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 89 0 51 42 100M = 51 0 TTCTTTCTGTTCATGTGTATTTGCTGTCTCTTAGCCCAGACTTCCCGTGTCCTTTCCACCGGGCCTTTGAGAGGTCACAGGGTCTTGATGCTGTGGTCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YT:Z:UP r0 165 0 51 0 * = 51 0 CAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP Flags for when mates align non-concordantly, with many alignments for one (fw:1, sam:1) @@ -16237,10 +16255,10 @@ >0 CAGCGGCTAGCTATCGATCGTCCGGCAGCTATCATTATGATAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCGAGGATAGATCGCTCGCCTGACCTATATCGCTCGCGATTACGAGCTACGTACTGGCTATCCGAGCTGACGCATCACGACGATCG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --large-index --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:290 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 3 1 38M = 163 202 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 0 163 1 42M = 3 -202 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) @@ -16248,67 +16266,67 @@ >0 CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0C39 YT:Z:UU MD:Z 1 (fw:0, sam:1) References: >0 CACGATCGACTTGACTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 15 -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 --debug --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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: >0 CACGATCGACTTGAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:54 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M1D40M * 0 0 CACGATCGACTTGGTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:13^A0A39 YT:Z:UU MD:Z 3 (fw:1, sam:1) References: >0 CACGATCGACTTGTAATCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 4 -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 --debug --large-index --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 13M2D40M * 0 0 CACGATCGACTTGCTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-17 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:13^TA0A39 YT:Z:UU MD:Z 4 (fw:1, sam:1) References: >0 CACGATCGACTTGNNNTCATCGACGCTATCATTAATATATATAAGCCCGCATCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:55 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 5 -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: @@ -16324,19 +16342,19 @@ >0 TTGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU Local alignment 1 (fw:0, sam:1) References: >0 TTGT -./bowtie2 --debug --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --policy "MIN=L,1.0,0.75" --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 4M * 0 0 TTGT IIII AS:i:8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:4 YT:Z:UU Local alignment 2 (fw:1, sam:1) References: @@ -16352,50 +16370,50 @@ References: >0 TTGA -./bowtie2 --debug --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 --debug --large-index --local --policy "MIN=L,1.0,0.75\;SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:4 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --policy MIN=L,1.0,0.75;SEED=0;SEEDLEN=3;IVAL=C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 3M1S * 0 0 TTGT IIII AS:i:6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU Local alignment 3 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 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 --debug --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -L 8 -i C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 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 --debug --large-index --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 --debug --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU r0 256 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU Local alignment 4 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0" --score-min=C,12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --policy SEED=0;SEEDLEN=3;IVAL=C,1,0 --score-min=C,12 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 37 12M * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:24 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:12 YT:Z:UU r0 272 0 9 255 8M4S * 0 0 TTGTTCGTTTGT IIIIIIIIIIII AS:i:16 XS:i:16 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU Alignment order -k (fw:1, sam:1) @@ -16403,10 +16421,10 @@ >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -16415,10 +16433,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --debug --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -k 4 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -16427,10 +16445,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --debug --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 @@ -16439,10 +16457,10 @@ References: >0 GCGCATGCACATATCANNNNNGCGCATGCACATATCTNNNNNNNNGCGCATGCACATATTTNNNNNNNNNGCGCATGGTGTTATCA -./bowtie2 --debug --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:86 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --min-score C,-24,0 -L 4 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 31 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:16 YT:Z:UU r0 272 0 22 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:15T0 YT:Z:UU r0 272 0 46 255 16M * 0 0 GCGCATGCACATATCA GOAIYEFGFIWDSFIU AS:i:-12 XS:i:-6 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:14T0T0 YT:Z:UU @@ -16452,10 +16470,10 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --debug --large-index --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 99 0 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 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 @@ -16486,10 +16504,10 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --debug --large-index --fr --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 83 0 169 1 19M = 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 r0 339 0 169 255 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP @@ -16520,11 +16538,11 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --debug --large-index --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --debug --large-index --fr --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:407 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" r0 99 0 3 1 19M = 169 185 CTATCATCACGCGGATATT IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 147 0 169 1 19M = 3 -185 TTAGGGGTAGACCCCCCCC IIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r1 83 0 270 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 @@ -16535,11 +16553,11 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNNNAGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAAATAGACGACTCGATCGCGGATTAGGGGTAGACCCCCCCCCGACTNNNNNNNNCGGTAATACGGCCATCGCGGCGGCATTACTCGGCGACTGCACGAGCAGATATTGGGGGTCTAATATAACGTCTCATTAAAACGCTCTAGTCAGCTCATTGGCTCTA -./bowtie2 --debug --large-index --fr --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 0 104 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 @@ -16551,22 +16569,22 @@ >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --large-index --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 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 --debug --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 +./bowtie2 --debug --large-index --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant (fw:1, sam:1) @@ -16584,198 +16602,198 @@ References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --large-index --ff --quiet -M 1 --no-discordant --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 --debug --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 3 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-discordant --no-mixed (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --no-discordant --no-mixed --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-dovetail (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 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 --debug --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 +./bowtie2 --debug --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --un-conc=.tmp.simple_tests.pl (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --un-conc=.tmp.simple_tests.pl --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q --passthrough -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP r0 179 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP Non-overlapping; --no-overlap (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 --debug --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 18M = 24 41 GCTATCATCACGCGGATA IIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:18 YS:i:0 YT:Z:CP r0 131 0 24 42 19M = 2 -41 CGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:19 YS:i:0 YT:Z:CP Non-overlapping; --no-overlap (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --large-index --no-overlap --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-overlap --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-dovetail --ff --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --no-contain --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-contain --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 67 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:CP r0 131 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:CP Overlapping; --no-contain (fw:0, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --large-index --no-contain --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --no-contain --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-contain --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-contain --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-overlap (fw:1, sam:1) References: >0 AGCTATCATCACGCGGATATTAGCGCATCGACATTAATATCCCCAAA -./bowtie2 --debug --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 --debug --large-index --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --no-overlap --ff --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 65 0 2 42 21M = 20 41 GCTATCATCACGCGGATATTA IIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:21 YS:i:0 YT:Z:DP r0 129 0 20 42 23M = 2 -41 TTAGCGCATCGACATTAATATCC IIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YS:i:0 YT:Z:DP Overlapping; --no-overlap (fw:0, sam:1) @@ -16794,183 +16812,183 @@ >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTCGCTGCGGGG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 1 -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 --debug --large-index --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:105 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 42 88M * 0 0 GCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTAATTTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfglduhiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YT:Z:UU Scoring params 2 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-38 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 3 (fw:1, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --debug --large-index --ignore-quals --rfg 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 --debug --large-index --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --rfg 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --rfg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-31 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 3 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --debug --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 +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --ignore-quals --rdg 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-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 --debug --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --rdg 1,2 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --mp 8 --score-min C,-40,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-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 --debug --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 --debug --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:102 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-41 XN:i:0 XM:i:2 XO:i:2 XG:i:7 NM:i:9 MD:Z:0G11A24^GACC44 YT:Z:UU Scoring params 6 (fw:0, sam:1) References: >0 ACTATTGCGCGCATGCACATATCAATTAAGCCGTCTCTCTAAAGAGACCCCAATCTCGCGCGCTAGACGTCAGTAGTTTTTTATAAACACCTCGCTGCGGGG -./bowtie2 --debug --large-index --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --ignore-quals --np 4 --score-min C,-41,0 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ignore-quals --np 4 --score-min C,-41,0 -N 1 -L 20 --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 37M4D30M3I14M * 0 0 NCGCATGCACATTTCAATTAAGCCGTCTCTCTAAAGACCAATCTCGCGCGCTAGACGTCAGTAGTTTAAATTTATAAACACCTC GOAIYEFGFIWDSFIUYWEHRIWQWLFNSLDKkjdfgiuevhsiuqkAUHFIUEHGIUDJFHSKseuweyriwfskdgbiuuhh AS:i:-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 --debug --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 +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIIA AS:i:-5 XS:i:-5 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 --debug --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 --debug --large-index -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII! AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a ! --mp 3,3 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --large-index -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 --debug --large-index -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -L 6 --mp 3,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT 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 --debug --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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: @@ -16986,151 +17004,151 @@ References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --large-index -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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a I --mp 3,6 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --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 --debug --large-index -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -L 6 --mp 6,3 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1a --ignore-quals (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --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 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --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 +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --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 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTGTTCGT IIIIIII5 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --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 +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-3 XS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c --ignore-quals (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --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 +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU Q XS:i 1c --ignore-quals (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --ignore-quals --quiet -M 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCGT IIIIIII4 AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:7A0 YT:Z:UU (fw:1, sam:1) References: >0 CATCGACTGAGACTCGTACGACAATTACGCGCATTATTCGCATCACCAGCGCGGCGCGCGCCCCCTAT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --large-index --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 73 0 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 --debug --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 +./bowtie2 --debug --large-index --fr --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:68 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 457 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:528 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,4,C,1,0 --quiet -M 1 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 289 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 1 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -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 --debug --large-index --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -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 --debug --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 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 0 8M * 0 0 TTGTTCGT 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 --debug --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 +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGT IIIIIIII YT:Z:UU XS:i 2 (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGA -./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-5 --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:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-5 --quiet --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACGAACAA IIIIIIII YT:Z:UU XS:i 3a (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3a (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3b (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=52 --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3c (fw:1, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --debug --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 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 3c (fw:0, sam:1) References: >0 TTGTTCGATTGTTCGT -./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,7,C,1 --score-min=C,-6 --seed=53 --quiet -M 2 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 39 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4a (fw:1, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=53 --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4a (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 4b (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGT -./bowtie2 --debug --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --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:24 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,6,C,1 --score-min=C,-12 --seed=54 --quiet -M 3 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5a (fw:1, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --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 --debug --large-index --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,6,C,1,1 --score-min=C,-12 --seed=54 --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5a (fw:0, sam:1) References: @@ -17361,166 +17379,166 @@ References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA -./bowtie2 --debug --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 --debug --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --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:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU XS:i 5b (fw:0, sam:1) References: >0 TTGTTCAATTGTTCGATTGTTCGTTTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAATTGTTCAA -./bowtie2 --debug --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:120 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --multiseed=0,5,C,1,1 --score-min=C,-12 --seed=55 --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 17 35 8M * 0 0 TTGTTCGT IIIIIIII AS:i:0 XS:i:-6 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:8 YT:Z:UU BWA-SW-like 1 (fw:1, sam:1) References: >0 GTTTAGATTCCACTACGCTAACCATCGAGAACTCGTCTCAGAGTTTCGATAGGAAAATCTGCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --bwa-sw-like --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --bwa-sw-like --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 3 -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 --debug --large-index --bwa-sw-like --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like --quiet -a --reads-per-batch 1 -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 --debug --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --large-index --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like -L 18 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:64 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --bwa-sw-like -i C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 4 255 26M3D27M * 0 0 TAGATTCCACTACGCTAACCATCGAGTCGTCTCAGAGTTTCGATAGGAAAATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:42 XN:i:0 XM:i:0 XO:i:1 XG:i:3 NM:i:3 MD:Z:26^AAC27 YT:Z:UU SAM paired-end where both alignments start at the same offset (fr case) (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 = 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 --debug --large-index --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 --debug --large-index --ff --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 = 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 --debug --large-index --rf --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --rf --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --rf --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --rf --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 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 --debug --large-index --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 --debug --large-index --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 4 255 24M = 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 --debug --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 +./bowtie2 --debug --large-index --rf --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --rf --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 4 255 24M = 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 --debug --large-index --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug --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 --debug --large-index --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --debug --large-index --fr --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:69 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CTATATACGAAAAAGCGTCGGCGA IIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 GATTGTCTTTTCCCGGAAAAATCGT IIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP SAM paired-end where both mates align, but discordantly (fw:1, sam:1) References: >0 GCACTATCTACGCTTCGGCGTCGGCGAAAAAACGCACGACCGGGTGTGTGACAATCATATATAGCGCGC -./bowtie2 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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) @@ -17542,30 +17560,30 @@ CCGGGTCGTCACGCCCCGCTTGCGTCANGCCCCTCACCCTCCCTTTGTCGGCTCCCACCCCTCCCCATCCGTTGTCCCCGCCCCCGCCCGCCGGGTCGTCACGCCCCGCTTGCGTCANGC >1 GCTCGGAATTCGTGCTCCGNCCCGTACGGTT -./bowtie2 --debug --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 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --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 +./bowtie2 --debug --large-index --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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 --debug --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 --debug --large-index --policy "MMP=R\;MIN=L,8.8,-8.1" --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=R;MIN=L,8.8,-8.1 --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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: @@ -17574,11 +17592,11 @@ >1 CCTTGTTNTTAATGCTGCCTGGTTTNG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy RDG=2.02030755427021,2.81949533273331;MIN=L,-6.52134769703939,-3.39889659588514;IVAL=L,0.127835912101927 --overhang --trim5 5 --fr --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 ACATATCCAGAGCTGCCGACAACGAAATGAACCCGAGAGCACAAATCCAGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP matchesRef regression 2 (fw:0, sam:1) @@ -17587,11 +17605,11 @@ GTTGTCGGCAGCTCTGGATATGTGNTCTCGGGTTTATNTCGTTGTCG >1 CCTTGTTNTTAATGCTGCCTGGTTTNG -./bowtie2 --debug --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 +./bowtie2 --debug --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 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:47 @SQ SN:1 LN:27 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 89 0 1 255 29S23M = 1 0 CTCTGGATTTGTGCTCTCGGGTTCATTTCGTTGTCGGCAGCTCTGGATATGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:-78 XN:i:7 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:23 YT:Z:UP r0 165 0 1 0 * = 1 0 CGGTTGCGAAGGCCCCTGGCGGTTGCTATGTCCTCTGGCGGTTGCGTTGTCGGCAGCTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII YT:Z:UP matchesRef regression 1 (fw:1, sam:1) @@ -17599,19 +17617,19 @@ >0 AGGTCGACCGAAAGGCCTAGAGGTCGACCGACAATCTGACCATGGGGCGAGGAGCGAGTAC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --overhang --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 11 -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 --debug --large-index --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --overhang --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:61 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 14 -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: @@ -17620,11 +17638,11 @@ >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --debug --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:23 @SQ SN:1 LN:28 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 65 0 4 255 10M 1 8 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 1 8 255 10M 0 4 0 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 65 0 4 255 10M 1 7 0 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP @@ -17635,11 +17653,11 @@ TTTATAAAAATATTTCCCCCCCC >1 CCCCCCTGTCGCTACCGCCCCCCCCCCC -./bowtie2 --debug --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 -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 @@ -17649,80 +17667,80 @@ >0 AGCATCGATCAGTATCTGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 7 -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 --debug --large-index -s 1 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --large-index -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 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 --debug --large-index -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --debug --large-index -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --large-index -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --debug --large-index -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --fr --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r1 83 0 10 255 10M = 1 -19 CAGTATCTGA IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r1 163 0 1 255 10M = 10 19 AGCATCGATC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --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 +./bowtie2 --debug --large-index -s 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --large-index -s 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 2 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -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 +./bowtie2 --debug --large-index -s 2 --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 2 --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" (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --debug --large-index -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 2 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 1 -u 1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz +./bowtie2 --debug --large-index -s 1 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 -u 1 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r1 0 0 4 255 11M * 0 0 ATCGATCAGTA IIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:11 YT:Z:UU (fw:0, sam:1) References: @@ -17737,142 +17755,142 @@ References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 0 0 4 255 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 --debug --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --large-index -s 1 --trim3 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --trim3 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --trim3 2 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 6 255 9M * 0 0 CGATCAGTA IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU (fw:0, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r1 16 0 4 255 9M * 0 0 ATCGATCAG IIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:9 YT:Z:UU (fw:1, sam:1) References: >0 AGCATCGATCAGTATCTGA -./bowtie2 --debug --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --large-index -s 1 --trim5 2 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:19 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -s 1 --trim5 2 --quiet -a --reads-per-batch 7 -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 --debug --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 --debug --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,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:3 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 8 -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 --debug --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,1,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:3 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 1S3M * 0 0 ATGC IIII AS:i:-1 XN:i:1 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:3 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --large-index --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGT -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-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 --debug --large-index --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --large-index --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 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 --debug --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 --debug --large-index --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 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 --debug --large-index --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --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 --debug --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r0 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 @@ -17880,10 +17898,10 @@ References: >0 TTGTTCGT -./bowtie2 --debug --large-index --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 --debug --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz" r0 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 @@ -17891,10 +17909,10 @@ References: >0 TTGTTCGT -./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" r0 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 @@ -17903,10 +17921,10 @@ References: >0 TTGTTCGT -./bowtie2 --debug --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 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz" r0 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 @@ -17915,91 +17933,91 @@ References: >0 TTGTTCGT -./bowtie2 --debug --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 --debug --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 +./bowtie2 --debug --large-index --overhang --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGT -./bowtie2 --debug --large-index --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --overhang --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --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 --debug --large-index --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --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:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M * 0 0 TTGTTCG IIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:7 YT:Z:UU 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 --debug --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.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 --debug --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -X 1000 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --fr --quiet -M 5 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 961 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 --debug --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 --debug --large-index -X 1000 --local --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 487 502 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 487 1 28M = 13 -502 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.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 --debug --large-index -X 1000 --local --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 --debug --large-index -X 1000 --local --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --local --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --local --fr --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --fr --quiet -k 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 = 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 @@ -18014,10 +18032,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --debug --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 +./bowtie2 --debug --large-index -X 1000 --fr --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --fr --quiet -k 5 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 961 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 r0 339 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP @@ -18032,10 +18050,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --debug --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --local --fr --quiet -k 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 1000 --local --fr --quiet -k 5 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 1 33M = 790 805 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 790 1 28M = 13 -805 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 355 0 13 255 33M = 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 @@ -18050,10 +18068,10 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACACACACCCCTATAGCTCGGAGCTGACTGGATCGACGACGT -./bowtie2 --debug --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 +./bowtie2 --debug --large-index -X 1000 --local --fr --quiet -k 5 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1000 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 0 961 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 r0 339 0 553 255 28M = 13 -568 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP @@ -18069,22 +18087,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -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 +./bowtie2 --debug --large-index -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 250 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 --debug --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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) @@ -18102,95 +18120,95 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --local -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 316 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 --debug --large-index -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 +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -X 150 --fr --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -k 1 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 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 --debug --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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 --debug --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.M.2.G. Paired -M 1 w/ 2 paired hit, 2 unpaired hits each, global (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --large-index --fr --quiet -M 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --fr --quiet -M 1 -X 150 --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:363 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -M 1 -X 150 --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --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 +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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 --debug --large-index --fr --quiet -M 1 --local -X 150 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -M 1 --local -X 150 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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 --debug --large-index --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 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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) @@ -18198,84 +18216,84 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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 --debug --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --fr --quiet -k 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --fr --quiet -k 1 -X 150 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP r0 147 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP P.k.1.L. Paired -k 1 w/ 1 paired hit, 1 unpaired hit each, local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --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 --debug --large-index --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -X 150 --fr --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 79 255 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:56 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:66 YT:Z:CP r0 163 0 13 255 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:56 YT:Z:CP P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -M 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 13 42 33M = 79 94 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YS:i:0 YT:Z:CP r0 147 0 79 42 28M = 13 -94 ACACACCCCTATAGCTCGGAGCTGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:28 YS:i:0 YT:Z:CP P.M.1.G. Paired -M w/ 1 paired hit, 1 unpaired hit each, global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGTATCGA -./bowtie2 --debug --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -X 150 --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index -X 150 --local --fr --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -X 150 --local --fr --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:126 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --local --fr --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --local --fr --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 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) @@ -18294,11 +18312,11 @@ References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGA -./bowtie2 --debug --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -X 150 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:2607 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --fr --quiet -M 5 --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 790 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) @@ -18306,22 +18324,22 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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.58.L. Unpaired -M 5 w/ 8 hits local (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGAGCGGTATCTACAGCCACTCATCACACACCCCTATAGCTCGGAGCTGACTGGGTTACTGGGGGGGATGCGTATCGACTATCGACAATATGACGCGTCGGTCACCCCATAATATGCAAAAATTATAGCTCACGACGCGTACTAATAGAAAACGCGCTATCAGCCTCCGACGCGGCGGTATCGAAGACGCAGTC -./bowtie2 --debug --large-index --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 +./bowtie2 --debug --large-index --local -X 150 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:1906 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local -X 150 --fr --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 1264 1 28M = 1198 -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 1198 1 33M = 1264 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) @@ -18329,233 +18347,233 @@ >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -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 --debug --large-index --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 42 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.L. Unpaired -M w/ 1 hit local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --debug --large-index --local --quiet -M 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --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:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 14 -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 --debug --large-index --local --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.k.1.G. Unpaired -k 1 w/ 1 hit global (fw:0, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --debug --large-index --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:56 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.1.L. Unpaired -m w/ 1 hit local (fw:1, sam:1) References: >0 AGACGCAGTCACCAGCGTACGGTATCTAGCTATGGGCATCGATCGACGACGTACGA -./bowtie2 --debug --large-index --local --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --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: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 --debug --large-index --local --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 13 255 33M * 0 0 CAGCGTACGGTATCTAGCTATGGGCATCGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:66 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:33 YT:Z:UU U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.G. Unpaired -M 1 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --local --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.2.L. Unpaired -M 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --local --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --quiet -M 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -M 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --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: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 --debug --large-index --quiet -k 1 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.G. Unpaired -k 1 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.2.L. Unpaired -k 1 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 2 --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.G. Unpaired -M 2 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -M 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 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: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 --debug --large-index --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -M 2 --local --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.22.L. Unpaired -M 2 w/ 2 hit local (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -M 2 --local --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 2 --local --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 256 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.22.G. Unpaired -k 2 w/ 2 hit global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 2 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 272 0 7 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.22.L. Unpaired -k 2 w/ 2 hit local (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --local --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --quiet -k 2 --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:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 2 --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 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 --debug --large-index --local --quiet -k 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:85 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 2 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 49 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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) @@ -18563,50 +18581,50 @@ >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -X 150 --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index -X 150 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 9 -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 --debug --large-index -X 150 --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index -X 150 --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -X 150 --quiet -M 5 --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --local --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 134 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.M.58.L. Unpaired -M 5 w/ 8 hits global (fw:0, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --local --quiet -M 5 --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -M 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 177 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU U.k.58.G. Unpaired -k 5 w/ 8 hits global (fw:1, sam:1) References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 5 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 @@ -18616,10 +18634,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 5 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 5 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 262 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 @@ -18629,10 +18647,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --local --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 219 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i: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 @@ -18642,10 +18660,10 @@ References: >0 AGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGAAGACGCAGATTACGGATCTACGATTCGAGTCGGTCAGTCACCAGCGTAAGATTACGGATCTACGATTCGAGTCGGTCAAGTGCGA -./bowtie2 --debug --large-index --local --quiet -k 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --local --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:340 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --local --quiet -k 5 --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 262 1 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 272 0 134 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU r0 272 0 92 255 30M * 0 0 AGATTACGGATCTACGATTCGAGTCGGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:60 XS:i:60 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:30 YT:Z:UU @@ -18656,39 +18674,39 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index -L 6 -i C,1,0 --policy "MMP=C27\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU r0 256 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C27;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 0 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU r0 272 0 1 255 8M * 0 0 TTGTTCAT IIIIIIII AS:i:-27 XS:i:-27 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6G1 YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 TTGTTCAT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 --debug --large-index -L 6 -i C,1,0 --policy "MMP=C28\;MIN=L,-3,-3\;RDG=25,15\;RFG=25,15" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -L 6 -i C,1,0 --policy MMP=C28;MIN=L,-3,-3;RDG=25,15;RFG=25,15 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATGAACAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: @@ -18719,10 +18737,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --debug --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz +./bowtie2 --debug --large-index --policy "SEED=1\;SEEDLEN=2" --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=1;SEEDLEN=2 --quiet -k 1 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 16 0 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 @@ -18744,205 +18762,205 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=29,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU Gap penalties 1 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=29,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 6M1D6M * 0 0 TTGTTCTTTGTT IIIIIIIIIIII AS:i:-39 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:6^G6 YT:Z:UU Gap penalties 2 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 TTGTTCTTTGTT IIIIIIIIIIII YT:Z:UU Gap penalties 2 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=30,10\;RFG=25,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=30,10;RFG=25,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 AACAAAGAACAA IIIIIIIIIIII YT:Z:UU Gap penalties 3 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --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 --debug --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 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 16 -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 --debug --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 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=30,16\;MIN=L,-3,-3" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=30,16;MIN=L,-3,-3 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU Gap penalties 5 (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII YT:Z:UU Gap penalties 5 (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "MMP=C30\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RDG=25,15\;RFG=31,15\;MIN=L,-3,-3" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=25,15;RFG=31,15;MIN=L,-3,-3 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 AACAAATCGAACAA IIIIIIIIIIIIII YT:Z:UU Gap penalties 6 (fw:1, sam:1) References: >0 ATTGTTCGTTTGTTCGTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --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 6 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 6 -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 --debug --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 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:18 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy MMP=C30;SEED=0;SEEDLEN=2;IVAL=C,1,0;RDG=19,10;RFG=18,10;MIN=L,-3,-3 --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:13 YT:Z:UU N filtering 2 (fw:1, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 2 (fw:0, sam:1) References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:1, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 3 (fw:0, sam:1) References: >0 GAGACTTTATACGCATCGAANTATCGCTCTA -./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 4 (fw:1, sam:1) References: >0 GAGACTTTNTACGCATCGAACTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 4 (fw:0, sam:1) References: >0 GAGACTTTNTACGCATCGAACTATCGCTCTA -./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "NCEIL=L,0,0" --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:31 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU N filtering 5 (fw:1, sam:1) References: @@ -18958,39 +18976,39 @@ References: >0 GAGACTTTATNCGCATCGAACTATCGCTCTA -./bowtie2 --debug --large-index --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 16 0 9 255 13M * 0 0 ATACGCATCGAAC IIIIIIIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:2N10 YT:Z:UU N filtering 6 (fw:1, sam:1) References: >0 GAGACTTTNTACGCATCGAANTATCGCTCTA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ATACGCATCGAAC IIIIIIIIIIIII YT:Z:UU N filtering 6 (fw:0, sam:1) References: >0 GAGACTTTNTACGCATCGAANTATCGCTCTA -./bowtie2 --debug --large-index --policy "NCEIL=L,0,0.1\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy NCEIL=L,0,0.1;SEED=0;SEEDLEN=2;IVAL=C,1,0 --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 GTTCGATGCGTAT IIIIIIIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTTTGTTCGTTTG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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: @@ -19006,66 +19024,66 @@ >0 TTGTTCGTTTGTT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 1 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 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 --debug --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 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C30\;RDG=25,15\;RFG=25,20\;MIN=L,-3,-3" --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:13 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C30;RDG=25,15;RFG=25,20;MIN=L,-3,-3 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 7M1I6M * 0 0 TTGTTCGATTTGTT IIIIIIIIIIIIII AS:i:-45 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:13 YT:Z:UU (fw:1, sam:1) References: >0 ACNCA ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU (fw:0, sam:1) References: >0 ACNCA -./bowtie2 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 4 255 2M * 0 0 CA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU N ceil = 0, 2 legit hits (1) (fw:1, sam:1) References: >0 ACNCA -./bowtie2 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:5 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 6 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --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 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 24 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 14 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -19074,10 +19092,10 @@ References: >0 ACNCANNNNNNNNCGNNNNNNNNCG -./bowtie2 --debug --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 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:25 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 @@ -19087,10 +19105,10 @@ >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 +./bowtie2 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 8 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -19101,10 +19119,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --debug --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 --debug --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:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 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 @@ -19115,10 +19133,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --debug --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 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,0,0" --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:37 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,0,0 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 32 1 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 24 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r0 256 0 32 255 2M * 0 0 CG II AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -19129,10 +19147,10 @@ References: >0 ACNCANNNNNNAACGNNNNNNNACGAANNNNCGAAAN -./bowtie2 --debug --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 @@ -19144,10 +19162,10 @@ >0 TTGTTYGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz +./bowtie2 --debug --large-index --quiet -a --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;NCEIL=L,2,0" --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:8 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --reads-per-batch 12 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz" r0 0 0 1 255 8M * 0 0 TTGTTGGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU r1 0 0 1 255 8M * 0 0 TTGTTCGT IIIIIIII AS:i:-1 XN:i:1 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5N2 YT:Z:UU (fw:1, sam:1) @@ -19164,39 +19182,39 @@ References: >0 ATAACCTTCG -./bowtie2 --debug --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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --overhang --gbar 3 --policy "MMP=C30\;RDG=5,5\;SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;RFG=25,20\;MIN=L,-3,-3" --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:10 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 10 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --overhang --gbar 3 --policy MMP=C30;RDG=5,5;SEED=0;SEEDLEN=2;IVAL=C,1,0;RFG=25,20;MIN=L,-3,-3 --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 255 4M2D4M * 0 0 ATAATTCG IIIIIIII AS:i:-15 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:4^CC4 YT:Z:UU (fw:1, sam:1) References: >0 ATATGCCCCATGCCCCCCTCCG ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --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 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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 5 -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 --debug --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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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 8 -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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 8 -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 --debug --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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 --debug --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" r0 65 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 129 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 65 0 4 255 10M = 30 36 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP @@ -19217,10 +19235,10 @@ References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCTGTCGCTACCGCCCCCCCCCCC -./bowtie2 --debug --large-index -I 0 -X 35 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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 --debug --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,.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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 35 --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz,.simple_tests.2c.fq.gz,.simple_tests.2d.fq.gz,.simple_tests.2e.fq.gz,.simple_tests.2f.fq.gz,.simple_tests.2g.fq.gz,.simple_tests.2h.fq.gz" r0 113 0 31 255 10M = 4 -37 GTCGCTACCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 113 0 30 255 10M = 4 -36 TGTCGCTACC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP @@ -19242,10 +19260,10 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz +./bowtie2 --debug --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 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 @@ -19254,10 +19272,10 @@ References: >0 TTTATAAAAATATTTCCCCCCCCCCCCCCGGGCCCGCCCGCCCCCCCCCCC -./bowtie2 --debug --large-index -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 +./bowtie2 --debug --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz -2 .simple_tests.2a.fq.gz,.simple_tests.2b.fq.gz" r0 113 0 31 255 10M = 4 -37 GGCCCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M = 31 37 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r1 115 0 28 255 10M = 4 -34 CCGGGCCCGC IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP @@ -19267,20 +19285,20 @@ >0 TTTATAAAAATATTTCCCCCCCCCCCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -I 0 -X 36 --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 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -I 0 -X 36 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:51 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 36 --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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) @@ -19288,20 +19306,20 @@ >0 TTTATAAAAATATTTCCCCCCGATCGCCCGCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -I 28 -X 80 --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:41 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 28 -X 80 --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 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 --debug --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:41 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 6 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 28 -X 80 --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 113 0 21 255 10M = 4 -27 CGATCGCCCG IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP r0 177 0 4 255 10M = 21 27 ATAAAAATAT IIIIIIIIII AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:DP Simple paired-end 9 (fw:1, sam:1) @@ -19309,22 +19327,22 @@ >0 CCCATATATATATCCTCCCATATATATATCCCTCCCCATATATATATCCCTTTTCCTTTCGCGCGCGCGTTTCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 99 0 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 --debug --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -M 2 --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 60 1 10M = 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) @@ -19332,10 +19350,10 @@ >0 CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -I 0 -X 80 --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 --debug --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 80 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 12 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 @@ -19346,10 +19364,10 @@ References: >0 CCCATATATATATCCTCCCATATATATATCCCTTCCCATATATATATCCCTTTTTTTTTCGCGCGCGCGTTTCCCCCCCCC -./bowtie2 --debug --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:81 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 8 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 80 --fr --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 83 0 60 1 10M = 20 -50 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 163 0 20 1 10M = 60 50 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 339 0 60 255 10M = 4 -66 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP @@ -19361,10 +19379,10 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCCCTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -I 0 -X 50 --nofw --ff --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -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 @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 50 --nofw --ff --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" 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) @@ -19372,20 +19390,20 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 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 --debug --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz +./bowtie2 --debug --large-index -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 2 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 50 --no-mixed --ff --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 77 * 0 0 * * 0 0 CCCCCGGGGG IIIIIIIIII YT:Z:UP r0 141 * 0 0 * * 0 0 ATATATATAT IIIIIIIIII YT:Z:UP Simple paired-end 1 (fw:1, sam:1) @@ -19393,20 +19411,20 @@ >0 CCCATATATATATCCCTTTTTTTCCCCCCCCTTTTCGCGCGCGCGTTTTCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index -I 0 -X 50 --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 --debug --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 50 --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 10 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 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 --debug --large-index -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 --debug --large-index -I 0 -X 50 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:53 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 -I 0 -X 50 --ff --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q -1 .simple_tests.1a.fq.gz -2 .simple_tests.2a.fq.gz" r0 115 0 36 255 10M = 4 -42 CGCGCGCGCG IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP r0 179 0 4 255 10M = 36 42 ATATATATAT IIIIIIIIII AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:10 YS:i:0 YT:Z:CP (fw:1, sam:1) @@ -19414,10 +19432,10 @@ >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --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 --debug --large-index --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 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 @@ -19438,10 +19456,10 @@ References: >0 AAAAAAAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCC -./bowtie2 --debug --large-index --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 --debug --large-index --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:49 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -k 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz,.simple_tests.1b.fq.gz,.simple_tests.1c.fq.gz,.simple_tests.1d.fq.gz,.simple_tests.1e.fq.gz,.simple_tests.1f.fq.gz,.simple_tests.1g.fq.gz,.simple_tests.1h.fq.gz,.simple_tests.1i.fq.gz,.simple_tests.1j.fq.gz,.simple_tests.1k.fq.gz,.simple_tests.1l.fq.gz,.simple_tests.1m.fq.gz,.simple_tests.1n.fq.gz,.simple_tests.1o.fq.gz,.simple_tests.1p.fq.gz" r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU r1 16 0 10 255 2M * 0 0 AA II AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:2 YT:Z:UU @@ -19463,104 +19481,104 @@ >0 TTGTTCGTTTGTTCGT ./bowtie2-build --large-index --quiet .simple_tests.pl.fa .simple_tests.tmp -./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 1 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 8 -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 --debug --large-index --quiet -M 1 --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -M 1 --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz Warning: -M is deprecated. Use -D and -R to adjust effort instead. @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -M 1 --reads-per-batch 9 -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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --overhang --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;NCEIL=L,2,0 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 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 --debug --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 +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 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 --debug --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 13 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --quiet -a --reads-per-batch 3 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 11 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --quiet -a --reads-per-batch 3 -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 --debug --large-index --policy SEED=0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0 --quiet -a --reads-per-batch 5 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 TTATTAGT IIIIIIII YT:Z:UU (fw:0, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --policy SEED=0 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 7 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=3;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:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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 --debug --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=3\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 14 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=3;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 15 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 4 * 0 0 * * 0 0 ACTAATAA IIIIIIII YT:Z:UU (fw:1, sam:1) References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 9 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --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" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 0 0 9 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 256 0 1 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 256 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU @@ -19571,10 +19589,10 @@ References: >0 TTGTTCGTTTGTTCGT -./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz +./bowtie2 --debug --large-index --policy "SEED=0\;SEEDLEN=2\;IVAL=C,1,0\;MMP=C1" --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz @HD VN:1.5 SO:unsorted GO:query @SQ SN:0 LN:16 -@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 16 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" +@PG ID:bowtie2 PN:bowtie2 VN:2.5.0 CL:"/build/bowtie2-2.5.0/bowtie2-align-l-debug --wrapper basic-0 --policy SEED=0;SEEDLEN=2;IVAL=C,1,0;MMP=C1 --quiet -a --reads-per-batch 4 -x .simple_tests.tmp -q .simple_tests.1a.fq.gz" r0 16 0 1 0 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 272 0 9 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-2 XS:i:-2 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:2G2C2 YT:Z:UU r0 272 0 5 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-3 XS:i:-2 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:1C0G2T2 YT:Z:UU @@ -19582,30 +19600,30 @@ r0 272 0 4 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C0G1T0T0G0 YT:Z:UU r0 272 0 8 255 8M * 0 0 TTATTAGT IIIIIIII AS:i:-5 XS:i:-2 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2T0G1T0C0G0 YT:Z:UU PASSED -make[2]: Leaving directory '/build/bowtie2-2.5.0' -make[1]: Leaving directory '/build/bowtie2-2.5.0' +make[2]: Map '/build/bowtie2-2.5.0' wordt verlaten +make[1]: Map '/build/bowtie2-2.5.0' wordt verlaten create-stamp debian/debhelper-build-stamp dh_prep dh_installdirs dh_auto_install make -j8 install DESTDIR=/build/bowtie2-2.5.0/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" -make[1]: Entering directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt binnengegaan mkdir -p /build/bowtie2-2.5.0/debian/tmp/usr/local/bin for file in bowtie2-build-s bowtie2-build-l bowtie2-align-s bowtie2-align-l bowtie2-inspect-s bowtie2-inspect-l bowtie2-inspect bowtie2-build bowtie2 ; do \ cp -f $file /build/bowtie2-2.5.0/debian/tmp/usr/local/bin ; \ done -make[1]: Leaving directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt verlaten debian/rules override_dh_install -make[1]: Entering directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt binnengegaan dh_install -X.gitignore -make[1]: Leaving directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt verlaten dh_installdocs debian/rules override_dh_installchangelogs -make[1]: Entering directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt binnengegaan dh_installchangelogs NEWS -make[1]: Leaving directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt verlaten debian/rules override_dh_installman -make[1]: Entering directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt binnengegaan mkdir -p /build/bowtie2-2.5.0/debian/bowtie2/usr/share/man/man1/ debian/help2man-wrapper bowtie2 "wrapper for bowtie2-align-*" debian/help2man-wrapper bowtie2-build "wrapper for bowtie2-build-*" @@ -19617,7 +19635,7 @@ debian/help2man-wrapper bowtie2-align-l "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences" debian/help2man-wrapper bowtie2-align-s "ultrafast and memory-efficient backend tool for aligning sequencing reads to long reference sequences" rm -f /build/bowtie2-2.5.0/debian/bowtie2/usr/bin/bowtie2-buildc -make[1]: Leaving directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt verlaten dh_perl dh_link dh_strip_nondeterminism @@ -19630,14 +19648,14 @@ dh_shlibdeps -a dh_installdeb debian/rules override_dh_gencontrol -make[1]: Entering directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt binnengegaan dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.7.4~rc2-2), " -make[1]: Leaving directory '/build/bowtie2-2.5.0' +make[1]: Map '/build/bowtie2-2.5.0' wordt verlaten dh_md5sums dh_builddeb -dpkg-deb: building package 'bowtie2-dbgsym' in '../bowtie2-dbgsym_2.5.0-3_arm64.deb'. -dpkg-deb: building package 'bowtie2' in '../bowtie2_2.5.0-3_arm64.deb'. -dpkg-deb: building package 'bowtie2-examples' in '../bowtie2-examples_2.5.0-3_all.deb'. +dpkg-deb: pakket 'bowtie2' wordt gebouwd in '../bowtie2_2.5.0-3_arm64.deb'. +dpkg-deb: pakket 'bowtie2-dbgsym' wordt gebouwd in '../bowtie2-dbgsym_2.5.0-3_arm64.deb'. +dpkg-deb: pakket 'bowtie2-examples' wordt gebouwd in '../bowtie2-examples_2.5.0-3_all.deb'. dpkg-genbuildinfo --build=binary -O../bowtie2_2.5.0-3_arm64.buildinfo dpkg-genchanges --build=binary -O../bowtie2_2.5.0-3_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -19645,12 +19663,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/29054/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/29054/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/30247 and its subdirectories -I: Current time: Tue Apr 11 02:23:49 -12 2023 -I: pbuilder-time-stamp: 1681223029 +I: removing directory /srv/workspace/pbuilder/29054 and its subdirectories +I: Current time: Tue May 14 11:41:46 +14 2024 +I: pbuilder-time-stamp: 1715636506