Diff of the two buildlogs: -- --- b1/build.log 2025-02-06 10:39:00.237280660 +0000 +++ b2/build.log 2025-02-06 10:50:09.370968861 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Wed Feb 5 22:34:25 -12 2025 -I: pbuilder-time-stamp: 1738838065 +I: Current time: Thu Mar 12 07:02:04 +14 2026 +I: pbuilder-time-stamp: 1773248524 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -40,52 +40,84 @@ dpkg-source: info: applying adding_opens_arg_for_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1220965/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3950228/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Mar 11 17:02 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3950228/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3950228/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='aae6d3e7da4e4666b80131ace0e3b068' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1220965' - PS1='# ' - PS2='> ' + INVOCATION_ID=8528e347f1f049738664ff9c5303114e + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3950228 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.mZAqxdcZ/pbuilderrc_80Ma --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mZAqxdcZ/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-11.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.mZAqxdcZ/pbuilderrc_MvUk --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.mZAqxdcZ/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-11.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1220965/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3950228/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -669,7 +701,7 @@ Get: 466 http://deb.debian.org/debian trixie/main arm64 r-base-core arm64 4.4.2-1 [28.0 MB] Get: 467 http://deb.debian.org/debian trixie/main arm64 r-cran-rjava arm64 1.0-11-1+b1 [709 kB] Get: 468 http://deb.debian.org/debian trixie/main arm64 testng all 6.9.12-4 [795 kB] -Fetched 375 MB in 2s (163 MB/s) +Fetched 375 MB in 3s (112 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (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 ... 19957 files and directories currently installed.) @@ -2199,8 +2231,8 @@ Setting up tzdata (2024b-6) ... Current default time zone: 'Etc/UTC' -Local time is now: Thu Feb 6 10:35:20 UTC 2025. -Universal Time is now: Thu Feb 6 10:35:20 UTC 2025. +Local time is now: Wed Mar 11 17:04:19 UTC 2026. +Universal Time is now: Wed Mar 11 17:04:19 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -2801,7 +2833,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && 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 > ../libgoby-java_3.3.1+dfsg2-11_source.changes +I: user script /srv/workspace/pbuilder/3950228/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3950228/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libgoby-java-3.3.1+dfsg2/ && 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 > ../libgoby-java_3.3.1+dfsg2-11_source.changes dpkg-buildpackage: info: source package libgoby-java dpkg-buildpackage: info: source version 3.3.1+dfsg2-11 dpkg-buildpackage: info: source distribution unstable @@ -2814,7 +2850,7 @@ bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done" mh_unpatchpoms -plibgoby-io-java jh_clean -Duplicate specification "unlink|u" for option "u" +Duplicate specification "u=s" for option "u" debian/rules override_dh_clean make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' dh_clean @@ -3676,14 +3712,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.040 s] -[INFO] Goby I/O ........................................... SUCCESS [ 20.042 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 22.036 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.135 s] +[INFO] Goby I/O ........................................... SUCCESS [ 54.132 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 49.422 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 42.247 s -[INFO] Finished at: 2025-02-05T22:36:26-12:00 +[INFO] Total time: 01:44 min +[INFO] Finished at: 2026-03-12T07:08:10+14:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' @@ -3842,24 +3878,24 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite -22:36:42.408 INFO RLoggerMainLoopCallback - +07:08:52.398 INFO RLoggerMainLoopCallback - -22:36:42.414 INFO RLoggerMainLoopCallback - R version 4.4.2 (2024-10-31) -- "Pile of Leaves" +07:08:52.416 INFO RLoggerMainLoopCallback - R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu -22:36:42.415 INFO RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY. +07:08:52.416 INFO RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. -22:36:42.415 INFO RLoggerMainLoopCallback - R is a collaborative project with many contributors. +07:08:52.416 INFO RLoggerMainLoopCallback - R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. -22:36:42.415 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or +07:08:52.416 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. @@ -3938,7 +3974,7 @@ SLF4J: Found binding in [jar:file:/usr/share/java/logback-classic.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory] -22:36:42.917 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. +07:08:53.694 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. 0 AAC 3 ACC 6 @@ -3967,19 +4003,19 @@ AAC 75 ACC 78 ATC 81 -AGC22:36:47.081 WARN MessageChunksWriter - Using chunk-size=10000 -22:36:47.081 WARN MessageChunksWriter - Using chunk-size=9 -22:36:47.086 WARN MessageChunksWriter - Using chunk-size=9 +AGC07:09:02.908 WARN MessageChunksWriter - Using chunk-size=10000 +07:09:02.908 WARN MessageChunksWriter - Using chunk-size=9 +07:09:02.920 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 660 Average bytes/logical entry: 16.923077 Number of bits/base 3.6590436 -22:36:47.089 WARN MessageChunksWriter - Using chunk-size=9 +07:09:02.923 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 685 Average bytes/logical entry: 17.564102 Number of bits/base 3.797644 -22:36:47.094 WARN MessageChunksWriter - Using chunk-size=9 +07:09:02.929 WARN MessageChunksWriter - Using chunk-size=9 Total logical entries written: 39 Total bytes written: 660 Average bytes/logical entry: 16.923077 @@ -4009,57 +4045,57 @@ [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - registering user defined contexts: [CpG] [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest [main] INFO org.campagnelab.goby.stats.AnnotationAveragingWriter - annotations test-data/vcf-averaging/annotations-1.tsv loaded. -22:36:47.222 INFO BullardUpperQuartileNormalization - normalization denominator 52289.9 for sample B-7 -22:36:47.222 INFO BullardUpperQuartileNormalization - normalization denominator 53253.2 for sample B-3 -22:36:47.222 INFO BullardUpperQuartileNormalization - normalization denominator 105268 for sample A-3 -22:36:47.222 INFO BullardUpperQuartileNormalization - normalization denominator 100658 for sample A-12 -22:36:47.223 INFO BullardUpperQuartileNormalization - normalization denominator 50845.1 for sample B-15 -22:36:47.223 INFO BullardUpperQuartileNormalization - normalization denominator 52014.7 for sample B-14 -22:36:47.223 INFO BullardUpperQuartileNormalization - normalization denominator 50982.7 for sample B-11 -22:36:47.223 INFO BullardUpperQuartileNormalization - normalization denominator 100865 for sample A-17 -22:36:47.223 INFO BullardUpperQuartileNormalization - normalization denominator 50501.1 for sample B-2 -22:36:47.223 INFO BullardUpperQuartileNormalization - normalization denominator 50638.7 for sample B-10 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 103548 for sample A-16 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 51051.5 for sample B-8 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 52358.7 for sample B-4 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 105406 for sample A-2 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 102378 for sample A-0 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 52014.7 for sample B-6 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 104511 for sample A-9 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 103273 for sample A-8 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 103410 for sample A-5 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 107126 for sample A-4 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 102172 for sample A-6 -22:36:47.224 INFO BullardUpperQuartileNormalization - normalization denominator 102378 for sample A-7 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 50157.1 for sample B-5 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 103754 for sample A-10 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 105406 for sample A-14 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 51601.9 for sample B-9 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 103066 for sample A-1 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 53253.2 for sample B-0 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 50363.5 for sample B-12 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 51464.3 for sample B-13 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 103479 for sample A-19 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 99075.7 for sample A-18 -22:36:47.225 INFO BullardUpperQuartileNormalization - normalization denominator 107607 for sample A-15 -22:36:47.226 INFO BullardUpperQuartileNormalization - normalization denominator 51189.1 for sample B-1 -22:36:47.226 INFO BullardUpperQuartileNormalization - normalization denominator 105130 for sample A-13 -22:36:47.226 INFO BullardUpperQuartileNormalization - normalization denominator 103892 for sample A-11 -22:36:47.226 INFO BullardUpperQuartileNormalization - normalization denominator 51670.7 for sample B-16 -22:36:47.226 INFO BullardUpperQuartileNormalization - normalization denominator 52565.2 for sample B-17 -22:36:47.226 INFO BullardUpperQuartileNormalization - normalization denominator 52289.9 for sample B-19 -22:36:47.226 INFO BullardUpperQuartileNormalization - normalization denominator 50501.1 for sample B-18 +07:09:03.199 INFO BullardUpperQuartileNormalization - normalization denominator 54564.2 for sample B-7 +07:09:03.211 INFO BullardUpperQuartileNormalization - normalization denominator 53850.0 for sample B-3 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 103343 for sample A-3 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 105772 for sample A-12 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 53921.4 for sample B-15 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 53564.3 for sample B-14 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 54135.7 for sample B-11 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 106414 for sample A-17 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 54849.9 for sample B-2 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 52421.6 for sample B-10 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 109843 for sample A-16 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 54492.8 for sample B-8 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 53350.1 for sample B-4 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 106629 for sample A-2 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 105415 for sample A-0 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 52493.0 for sample B-6 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 105986 for sample A-9 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 107914 for sample A-8 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 109200 for sample A-5 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 106414 for sample A-4 +07:09:03.212 INFO BullardUpperQuartileNormalization - normalization denominator 106557 for sample A-6 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 108129 for sample A-7 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 53635.8 for sample B-5 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 108986 for sample A-10 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 104629 for sample A-14 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 52421.6 for sample B-9 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 109914 for sample A-1 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 53992.8 for sample B-0 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 54064.3 for sample B-12 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 53564.3 for sample B-13 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 108200 for sample A-19 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 109200 for sample A-18 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 110343 for sample A-15 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 52350.2 for sample B-1 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 111128 for sample A-13 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 105843 for sample A-11 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 53635.8 for sample B-16 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 53421.5 for sample B-17 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 52350.2 for sample B-19 +07:09:03.213 INFO BullardUpperQuartileNormalization - normalization denominator 54421.4 for sample B-18 Creating base test directory: test-results/stats-writer -allele: A ref: [CC] alt: [T]22:36:47.291 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -22:36:47.327 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -22:36:47.327 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -22:36:47.340 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -22:36:47.340 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -22:36:47.479 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -22:36:47.517 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. -22:36:47.517 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -22:36:47.626 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -22:36:47.646 INFO FDRAdjustment - ... statistic another-p-value-Bonferroni-adjusted was found, FDR adjustment executed. +allele: A ref: [CC] alt: [T]07:09:03.368 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +07:09:03.473 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +07:09:03.475 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +07:09:03.507 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +07:09:03.513 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +07:09:03.792 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +07:09:03.871 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. +07:09:03.871 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +07:09:04.091 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +07:09:04.132 INFO FDRAdjustment - ... statistic another-p-value-Bonferroni-adjusted was found, FDR adjustment executed. list3:element-id p-value p-value-BH-FDR-q-value [ 0 [2.354054E-7, 1.177027E-5] ] [ 1 [2.10159E-5, 4.294736666666667E-4] ] @@ -4113,7 +4149,7 @@ [ 49 [0.943789, 0.943789] ] element-id average RPKM group A(AC) average RPKM group B(AC) average log2_RPKM group A(AC) average log2_RPKM group B(AC) average count group A average count group B -[ id-1 [1.0059587527800717, 0.50270627580073, 0.008571151684586017, -0.9922123950920476, 0.0, 0.0] ] +[ id-1 [1.0010712163880322, 0.500898129922377, 0.0015446114118292948, -0.9974108695098528, 0.0, 0.0] ] truncated fdr=3.53108e-05 original=3.53108e-05 truncated fdr=0.00128842 original=0.00128842 @@ -4218,34 +4254,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:00.822 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:35.622 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:00.826 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:35.629 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:00.829 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:35.641 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:00.832 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:35.643 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:00.834 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:35.646 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:00.837 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:35.649 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:00.840 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:35.652 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:00.842 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:35.657 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:00.845 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:35.659 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:00.847 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:35.663 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4275,34 +4311,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:00.948 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:35.910 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:00.950 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:35.916 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:00.952 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:35.919 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:00.954 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:35.925 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:00.956 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:35.932 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:00.958 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:35.934 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:00.987 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:35.945 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:00.990 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:35.947 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:00.992 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:35.950 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:00.994 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:35.961 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4332,34 +4368,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.075 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:36.172 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.077 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:36.174 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.079 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:36.181 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.081 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:36.191 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.083 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:36.194 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.085 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:36.200 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.086 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:36.202 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.088 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:36.213 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.090 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:36.215 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.092 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:36.225 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4389,34 +4425,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.164 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:36.418 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.166 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:36.424 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.168 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:36.426 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.170 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:36.440 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.171 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:36.443 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.173 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:36.445 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.175 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:36.467 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.177 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:36.470 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.179 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:36.472 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.180 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:36.474 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4446,34 +4482,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.249 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:36.718 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.251 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:36.728 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.253 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:36.730 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.254 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:36.732 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.256 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:36.734 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.257 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:36.744 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.286 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:36.746 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.288 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:36.752 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.290 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:36.755 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.292 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:36.758 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4503,34 +4539,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.362 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:36.945 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.364 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:36.951 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.366 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:36.954 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.367 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:36.960 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.369 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:36.962 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.371 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:36.972 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.372 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:36.974 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.374 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:36.980 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.375 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:36.982 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.377 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:36.992 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4560,34 +4596,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.437 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:37.167 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.439 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:37.169 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.440 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:37.171 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.442 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:37.173 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.444 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:37.175 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.445 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:37.181 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.447 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:37.182 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.449 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:37.185 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.450 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:37.187 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.452 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:37.189 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4617,34 +4653,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.513 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:37.309 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.515 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:37.310 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.517 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:37.316 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.518 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:37.318 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.520 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:37.319 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.521 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:37.329 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.523 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:37.330 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.524 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:37.332 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.526 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:37.333 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.527 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:37.335 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4674,34 +4710,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.587 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:37.489 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.588 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:37.490 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.590 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:37.496 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.591 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:37.498 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.593 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:37.499 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.594 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:37.505 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.596 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:37.506 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.597 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:37.512 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.599 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:37.514 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.600 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:37.520 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4731,34 +4767,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.657 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:37.645 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.659 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:37.647 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.660 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:37.655 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.662 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:37.656 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.663 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:37.657 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.665 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:37.659 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.667 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:37.661 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.668 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:37.662 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.670 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:37.664 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.671 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:37.666 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4788,34 +4824,34 @@ #count(allele) < (2 *#filtered) [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.726 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:37.822 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.727 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:37.832 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.728 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:37.834 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.730 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:37.843 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.731 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:37.845 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.733 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:37.847 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.734 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:37.848 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.767 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:37.850 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.769 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:37.860 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.771 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:37.862 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 Associating basename: basen0 to group: A @@ -4844,34 +4880,34 @@ [main] INFO org.campagnelab.goby.stats.EmpiricalPValueEstimator - Setting statistic from dynamic option: ptest_mci [main] ERROR org.campagnelab.goby.alignments.IterateSortedAlignments - Genome reference no-name0 length (96) differs from alignment reference length (10000) for sequence target1 at index 0 [main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences -22:37:01.840 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +07:09:38.025 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen0 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen0 -22:37:01.841 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. +07:09:38.027 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen1.tmh has no 'too many hits' information (test-results/discover-variants/basen1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen1 -22:37:01.842 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. +07:09:38.036 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen2.tmh has no 'too many hits' information (test-results/discover-variants/basen2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen2 -22:37:01.844 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. +07:09:38.038 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen3.tmh has no 'too many hits' information (test-results/discover-variants/basen3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen3 -22:37:01.845 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. +07:09:38.043 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen4.tmh has no 'too many hits' information (test-results/discover-variants/basen4.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen4 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen4 -22:37:01.847 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. +07:09:38.045 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen5.tmh has no 'too many hits' information (test-results/discover-variants/basen5.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen5 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen5 -22:37:01.848 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. +07:09:38.047 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen6.tmh has no 'too many hits' information (test-results/discover-variants/basen6.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen6 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen6 -22:37:01.849 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. +07:09:38.052 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen7.tmh has no 'too many hits' information (test-results/discover-variants/basen7.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen7 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen7 -22:37:01.851 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. +07:09:38.054 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen8.tmh has no 'too many hits' information (test-results/discover-variants/basen8.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen8 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen8 -22:37:01.852 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. +07:09:38.064 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 info: + ref: A s=0 @@ -5031,187 +5067,224 @@ Number of targets: 45 peak : start :5 count :13 length :100010 peak : start :100020 count :10 length :1 -Appending count: 40433 length: 2 -Appending count: 47620 length: 9 -Appending count: 48167 length: 5 -Appending count: 18374 length: 4 -Appending count: 46016 length: 1 -Appending count: 18364 length: 9 -Appending count: 17887 length: 7 -Appending count: 15201 length: 7 -Appending count: 22620 length: 2 -Appending count: 36645 length: 7 -Appending count: 8120 length: 2 -Appending count: 35691 length: 2 -Appending count: 33069 length: 7 -Appending count: 1421 length: 10 -Appending count: 4068 length: 3 -Appending count: 16015 length: 2 -Appending count: 4384 length: 2 -Appending count: 31329 length: 6 -Appending count: 37736 length: 6 -Appending count: 30509 length: 3 -Appending count: 21378 length: 1 -Appending count: 31633 length: 1 -Appending count: 3307 length: 7 -Appending count: 20983 length: 10 -Appending count: 33523 length: 7 -Appending count: 23343 length: 5 -Appending count: 885 length: 7 -Appending count: 2990 length: 5 -Appending count: 31796 length: 9 -Appending count: 30976 length: 3 - position= 0 count= 40433 - position= 1 count= 40433 - position= 2 count= 47620 - position= 3 count= 47620 - position= 4 count= 47620 - position= 5 count= 47620 - position= 6 count= 47620 - position= 7 count= 47620 - position= 8 count= 47620 - position= 9 count= 47620 - position= 10 count= 47620 - position= 11 count= 48167 - position= 12 count= 48167 - position= 13 count= 48167 - position= 14 count= 48167 - position= 15 count= 48167 - position= 16 count= 18374 - position= 17 count= 18374 - position= 18 count= 18374 - position= 19 count= 18374 - position= 20 count= 46016 - position= 21 count= 18364 - position= 22 count= 18364 - position= 23 count= 18364 - position= 24 count= 18364 - position= 25 count= 18364 - position= 26 count= 18364 - position= 27 count= 18364 - position= 28 count= 18364 - position= 29 count= 18364 - position= 30 count= 17887 - position= 31 count= 17887 - position= 32 count= 17887 - position= 33 count= 17887 - position= 34 count= 17887 - position= 35 count= 17887 - position= 36 count= 17887 - position= 37 count= 15201 - position= 38 count= 15201 - position= 39 count= 15201 - position= 40 count= 15201 - position= 41 count= 15201 - position= 42 count= 15201 - position= 43 count= 15201 - position= 44 count= 22620 - position= 45 count= 22620 - position= 46 count= 36645 - position= 47 count= 36645 - position= 48 count= 36645 - position= 49 count= 36645 - position= 50 count= 36645 - position= 51 count= 36645 - position= 52 count= 36645 - position= 53 count= 8120 - position= 54 count= 8120 - position= 55 count= 35691 - position= 56 count= 35691 - position= 57 count= 33069 - position= 58 count= 33069 - position= 59 count= 33069 - position= 60 count= 33069 - position= 61 count= 33069 - position= 62 count= 33069 - position= 63 count= 33069 - position= 64 count= 1421 - position= 65 count= 1421 - position= 66 count= 1421 - position= 67 count= 1421 - position= 68 count= 1421 - position= 69 count= 1421 - position= 70 count= 1421 - position= 71 count= 1421 - position= 72 count= 1421 - position= 73 count= 1421 - position= 74 count= 4068 - position= 75 count= 4068 - position= 76 count= 4068 - position= 77 count= 16015 - position= 78 count= 16015 - position= 79 count= 4384 - position= 80 count= 4384 - position= 81 count= 31329 - position= 82 count= 31329 - position= 83 count= 31329 - position= 84 count= 31329 - position= 85 count= 31329 - position= 86 count= 31329 - position= 87 count= 37736 - position= 88 count= 37736 - position= 89 count= 37736 - position= 90 count= 37736 - position= 91 count= 37736 - position= 92 count= 37736 - position= 93 count= 30509 - position= 94 count= 30509 - position= 95 count= 30509 - position= 96 count= 21378 - position= 97 count= 31633 - position= 98 count= 3307 - position= 99 count= 3307 - position= 100 count= 3307 - position= 101 count= 3307 - position= 102 count= 3307 - position= 103 count= 3307 - position= 104 count= 3307 - position= 105 count= 20983 - position= 106 count= 20983 - position= 107 count= 20983 - position= 108 count= 20983 - position= 109 count= 20983 - position= 110 count= 20983 - position= 111 count= 20983 - position= 112 count= 20983 - position= 113 count= 20983 - position= 114 count= 20983 - position= 115 count= 33523 - position= 116 count= 33523 - position= 117 count= 33523 - position= 118 count= 33523 - position= 119 count= 33523 - position= 120 count= 33523 - position= 121 count= 33523 - position= 122 count= 23343 - position= 123 count= 23343 - position= 124 count= 23343 - position= 125 count= 23343 - position= 126 count= 23343 - position= 127 count= 885 - position= 128 count= 885 - position= 129 count= 885 - position= 130 count= 885 - position= 131 count= 885 - position= 132 count= 885 - position= 133 count= 885 - position= 134 count= 2990 - position= 135 count= 2990 - position= 136 count= 2990 - position= 137 count= 2990 - position= 138 count= 2990 - position= 139 count= 31796 - position= 140 count= 31796 - position= 141 count= 31796 - position= 142 count= 31796 - position= 143 count= 31796 - position= 144 count= 31796 - position= 145 count= 31796 - position= 146 count= 31796 - position= 147 count= 31796 - position= 148 count= 30976 - position= 149 count= 30976 - position= 150 count= 30976 +Appending count: 36864 length: 7 +Appending count: 6085 length: 8 +Appending count: 26617 length: 5 +Appending count: 14710 length: 3 +Appending count: 7644 length: 4 +Appending count: 31682 length: 9 +Appending count: 4349 length: 10 +Appending count: 6883 length: 7 +Appending count: 7364 length: 9 +Appending count: 27974 length: 9 +Appending count: 10843 length: 4 +Appending count: 5335 length: 7 +Appending count: 9926 length: 5 +Appending count: 32213 length: 1 +Appending count: 44 length: 9 +Appending count: 13924 length: 5 +Appending count: 45140 length: 1 +Appending count: 29138 length: 8 +Appending count: 39979 length: 3 +Appending count: 8497 length: 3 +Appending count: 2866 length: 9 +Appending count: 33907 length: 3 +Appending count: 45412 length: 10 +Appending count: 44228 length: 4 +Appending count: 2725 length: 8 +Appending count: 44497 length: 7 +Appending count: 44214 length: 10 +Appending count: 8278 length: 6 +Appending count: 32596 length: 6 +Appending count: 47285 length: 8 + position= 0 count= 36864 + position= 1 count= 36864 + position= 2 count= 36864 + position= 3 count= 36864 + position= 4 count= 36864 + position= 5 count= 36864 + position= 6 count= 36864 + position= 7 count= 6085 + position= 8 count= 6085 + position= 9 count= 6085 + position= 10 count= 6085 + position= 11 count= 6085 + position= 12 count= 6085 + position= 13 count= 6085 + position= 14 count= 6085 + position= 15 count= 26617 + position= 16 count= 26617 + position= 17 count= 26617 + position= 18 count= 26617 + position= 19 count= 26617 + position= 20 count= 14710 + position= 21 count= 14710 + position= 22 count= 14710 + position= 23 count= 7644 + position= 24 count= 7644 + position= 25 count= 7644 + position= 26 count= 7644 + position= 27 count= 31682 + position= 28 count= 31682 + position= 29 count= 31682 + position= 30 count= 31682 + position= 31 count= 31682 + position= 32 count= 31682 + position= 33 count= 31682 + position= 34 count= 31682 + position= 35 count= 31682 + position= 36 count= 4349 + position= 37 count= 4349 + position= 38 count= 4349 + position= 39 count= 4349 + position= 40 count= 4349 + position= 41 count= 4349 + position= 42 count= 4349 + position= 43 count= 4349 + position= 44 count= 4349 + position= 45 count= 4349 + position= 46 count= 6883 + position= 47 count= 6883 + position= 48 count= 6883 + position= 49 count= 6883 + position= 50 count= 6883 + position= 51 count= 6883 + position= 52 count= 6883 + position= 53 count= 7364 + position= 54 count= 7364 + position= 55 count= 7364 + position= 56 count= 7364 + position= 57 count= 7364 + position= 58 count= 7364 + position= 59 count= 7364 + position= 60 count= 7364 + position= 61 count= 7364 + position= 62 count= 27974 + position= 63 count= 27974 + position= 64 count= 27974 + position= 65 count= 27974 + position= 66 count= 27974 + position= 67 count= 27974 + position= 68 count= 27974 + position= 69 count= 27974 + position= 70 count= 27974 + position= 71 count= 10843 + position= 72 count= 10843 + position= 73 count= 10843 + position= 74 count= 10843 + position= 75 count= 5335 + position= 76 count= 5335 + position= 77 count= 5335 + position= 78 count= 5335 + position= 79 count= 5335 + position= 80 count= 5335 + position= 81 count= 5335 + position= 82 count= 9926 + position= 83 count= 9926 + position= 84 count= 9926 + position= 85 count= 9926 + position= 86 count= 9926 + position= 87 count= 32213 + position= 88 count= 44 + position= 89 count= 44 + position= 90 count= 44 + position= 91 count= 44 + position= 92 count= 44 + position= 93 count= 44 + position= 94 count= 44 + position= 95 count= 44 + position= 96 count= 44 + position= 97 count= 13924 + position= 98 count= 13924 + position= 99 count= 13924 + position= 100 count= 13924 + position= 101 count= 13924 + position= 102 count= 45140 + position= 103 count= 29138 + position= 104 count= 29138 + position= 105 count= 29138 + position= 106 count= 29138 + position= 107 count= 29138 + position= 108 count= 29138 + position= 109 count= 29138 + position= 110 count= 29138 + position= 111 count= 39979 + position= 112 count= 39979 + position= 113 count= 39979 + position= 114 count= 8497 + position= 115 count= 8497 + position= 116 count= 8497 + position= 117 count= 2866 + position= 118 count= 2866 + position= 119 count= 2866 + position= 120 count= 2866 + position= 121 count= 2866 + position= 122 count= 2866 + position= 123 count= 2866 + position= 124 count= 2866 + position= 125 count= 2866 + position= 126 count= 33907 + position= 127 count= 33907 + position= 128 count= 33907 + position= 129 count= 45412 + position= 130 count= 45412 + position= 131 count= 45412 + position= 132 count= 45412 + position= 133 count= 45412 + position= 134 count= 45412 + position= 135 count= 45412 + position= 136 count= 45412 + position= 137 count= 45412 + position= 138 count= 45412 + position= 139 count= 44228 + position= 140 count= 44228 + position= 141 count= 44228 + position= 142 count= 44228 + position= 143 count= 2725 + position= 144 count= 2725 + position= 145 count= 2725 + position= 146 count= 2725 + position= 147 count= 2725 + position= 148 count= 2725 + position= 149 count= 2725 + position= 150 count= 2725 + position= 151 count= 44497 + position= 152 count= 44497 + position= 153 count= 44497 + position= 154 count= 44497 + position= 155 count= 44497 + position= 156 count= 44497 + position= 157 count= 44497 + position= 158 count= 44214 + position= 159 count= 44214 + position= 160 count= 44214 + position= 161 count= 44214 + position= 162 count= 44214 + position= 163 count= 44214 + position= 164 count= 44214 + position= 165 count= 44214 + position= 166 count= 44214 + position= 167 count= 44214 + position= 168 count= 8278 + position= 169 count= 8278 + position= 170 count= 8278 + position= 171 count= 8278 + position= 172 count= 8278 + position= 173 count= 8278 + position= 174 count= 32596 + position= 175 count= 32596 + position= 176 count= 32596 + position= 177 count= 32596 + position= 178 count= 32596 + position= 179 count= 32596 + position= 180 count= 47285 + position= 181 count= 47285 + position= 182 count= 47285 + position= 183 count= 47285 + position= 184 count= 47285 + position= 185 count= 47285 + position= 186 count= 47285 + position= 187 count= 47285 loading transition for reader[0] position=0 length=1 count=0 loading transition for reader[1] position=0 length=6 count=1 (0,1) @@ -5255,11 +5328,11 @@ loading transition for reader[0] position=12 length=1 count=1 loading transition for reader[0] position=13 length=3 count=0 loading transition for reader[0] position=16 length=1 count=1 -22:37:03.228 WARN WiggleWindow - Not writing 101 7 -22:37:03.228 WARN WiggleWindow - Not writing 111 7 -22:37:03.228 WARN WiggleWindow - Not writing 131 8 -22:37:03.228 WARN WiggleWindow - Not writing 141 8 -22:37:03.228 WARN WiggleWindow - Not writing 151 8 +07:09:41.823 WARN WiggleWindow - Not writing 101 7 +07:09:41.837 WARN WiggleWindow - Not writing 111 7 +07:09:41.837 WARN WiggleWindow - Not writing 131 8 +07:09:41.837 WARN WiggleWindow - Not writing 141 8 +07:09:41.837 WARN WiggleWindow - Not writing 151 8 appending (count=0,length=1) appending (count=4,length=3) appending (count=1,length=3) @@ -5328,7 +5401,7 @@ appending (count=2,length=8) Hello appending (count=10,length=4) -22:37:03.247 WARN MessageChunksWriter - Using chunk-size=2 +07:09:41.919 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 0 Total bytes written: 31 Average bytes/logical entry: Infinity @@ -5337,7 +5410,7 @@ Number of queries: 2 Number of targets: 0 97 -22:37:03.254 WARN MessageChunksWriter - Using chunk-size=2 +07:09:41.939 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -5345,7 +5418,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.261 WARN MessageChunksWriter - Using chunk-size=2 +07:09:41.975 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -5353,7 +5426,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.265 WARN MessageChunksWriter - Using chunk-size=2 +07:09:41.988 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -5361,7 +5434,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.268 WARN MessageChunksWriter - Using chunk-size=2 +07:09:42.000 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -5369,10 +5442,10 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.274 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.279 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.290 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.292 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.017 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.035 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.070 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.072 WARN MessageChunksWriter - Using chunk-size=1000 0 23 Setting quality threshold to 0.02 @@ -5451,7 +5524,7 @@ read_index: 20 } -22:37:03.318 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.102 WARN MessageChunksWriter - Using chunk-size=1000 Total logical entries written: 20000 Total bytes written: 77210 Average bytes/logical entry: 3.8605 @@ -5459,15 +5532,15 @@ Max query index: 1999 Number of queries: 2000 Number of targets: 10 -22:37:03.387 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.389 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.390 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.398 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.399 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.401 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.408 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.409 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.411 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.227 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.228 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.229 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.240 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.241 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.243 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.252 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.254 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.255 WARN MessageChunksWriter - Using chunk-size=1000 entry.position(): 1 entry.position(): 2 entry.position(): 3 @@ -5480,24 +5553,24 @@ entry.position(): 10 entry.position(): 12 entry.position(): 99 -22:37:03.420 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.421 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.423 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.433 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.434 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.435 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.437 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-1.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-1.tmh does not exist). Assuming no queries have too many hits. +07:09:42.265 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.266 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.268 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.286 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.288 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.289 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.297 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-1.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-1.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-1 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-1 -22:37:03.439 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-2.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-2.tmh does not exist). Assuming no queries have too many hits. +07:09:42.299 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-2.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-2.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-2 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-2 -22:37:03.440 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-3.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-3.tmh does not exist). Assuming no queries have too many hits. +07:09:42.309 INFO AlignmentTooManyHitsReader - basename test-results/sort-concat/sort-concat-3.tmh has no 'too many hits' information (test-results/sort-concat/sort-concat-3.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/sort-concat/sort-concat-3 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/sort-concat/sort-concat-3 -22:37:03.444 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.445 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.446 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.313 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.314 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.315 WARN MessageChunksWriter - Using chunk-size=1000 Processing queryIndex=8 with description '8 perfect start of ref' Processing queryIndex=9 with description '9 perfect start of ref reverse strand' Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1' @@ -5524,7 +5597,7 @@ Processing queryIndex=5 with description '5 insertion on reverse strand' Processing queryIndex=10 with description '10 perfect end of ref' Processing queryIndex=11 with description '11 perfect end of ref reverse strand' -22:37:03.474 WARN MessageChunksWriter - Using chunk-size=2 +07:09:42.361 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5532,7 +5605,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.479 WARN MessageChunksWriter - Using chunk-size=2 +07:09:42.365 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5540,7 +5613,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.482 WARN MessageChunksWriter - Using chunk-size=2 +07:09:42.370 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5548,7 +5621,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.486 WARN MessageChunksWriter - Using chunk-size=2 +07:09:42.374 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5556,7 +5629,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.489 WARN MessageChunksWriter - Using chunk-size=2 +07:09:42.386 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5564,7 +5637,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.492 WARN MessageChunksWriter - Using chunk-size=2 +07:09:42.394 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5572,7 +5645,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.496 WARN MessageChunksWriter - Using chunk-size=2 +07:09:42.403 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -5580,45 +5653,45 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -22:37:03.502 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.427 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.505 WARN MessageChunksWriter - Using chunk-size=1 -22:37:03.510 WARN MessageChunksWriter - Using chunk-size=1 -22:37:03.513 WARN MessageChunksWriter - Using chunk-size=1 -22:37:03.517 WARN MessageChunksWriter - Using chunk-size=1 -22:37:03.523 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.525 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.435 WARN MessageChunksWriter - Using chunk-size=1 +07:09:42.443 WARN MessageChunksWriter - Using chunk-size=1 +07:09:42.447 WARN MessageChunksWriter - Using chunk-size=1 +07:09:42.451 WARN MessageChunksWriter - Using chunk-size=1 +07:09:42.466 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.468 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 Scanned 5 entries -22:37:03.531 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.532 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.474 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.476 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=30.0000 readOriginIndex=0 entry: score=30.0000 readOriginIndex=0 Scanned 2 entries -22:37:03.536 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.537 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.542 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.543 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.548 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.550 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.480 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.481 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.487 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.488 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.493 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.495 WARN MessageChunksWriter - Using chunk-size=1000 0 2 -22:37:03.555 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.556 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.502 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.503 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-101 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-101 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/alignments/concat/concat-align-102 [main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/alignments/concat/concat-align-102 -22:37:03.562 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.563 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.568 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.569 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.574 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.575 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.509 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.510 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.517 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.518 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.524 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.525 WARN MessageChunksWriter - Using chunk-size=1000 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 entry: score=50.0000 readOriginIndex=3 @@ -5647,25 +5720,25 @@ read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT -22:37:03.591 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.630 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.631 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.660 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.554 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.594 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.595 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.629 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -22:37:03.688 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.690 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.697 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.721 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.721 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.656 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.658 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.666 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.688 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.688 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -22:37:03.721 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.688 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 4ms; used/avail/free/total/max mem: 882.52M/14.90G/258.33M/1.14G/15.78G -22:37:03.729 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 3ms; used/avail/free/total/max mem: 153.12M/15.63G/132.09M/285.21M/15.78G +07:09:42.695 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 position: 19991 @@ -5746,36 +5819,36 @@ multiplicity: 1 query_length: 35 -22:37:03.761 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.765 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.787 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.787 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.787 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.788 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.726 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.730 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.757 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.757 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.757 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.757 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -22:37:03.788 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.788 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.757 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.757 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 932.86M/14.85G/207.99M/1.14G/15.78G -22:37:03.790 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.802 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:03.829 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.852 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.853 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.875 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 203.45M/15.58G/81.76M/285.21M/15.78G +07:09:42.760 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.774 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:42.856 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.885 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.886 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.916 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -22:37:03.898 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:03.899 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.943 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:42.945 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item]; used/avail/free/total/max mem: 1.02G/14.76G/119.05M/1.14G/15.78G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 106.14M/15.67G/179.08M/285.21M/15.78G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -5904,25 +5977,25 @@ multiplicity: 1 query_length: 35 -22:37:03.978 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.001 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.003 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.025 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.118 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.194 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.207 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.260 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -22:37:04.047 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.048 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.051 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. -22:37:04.056 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. -22:37:04.056 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +07:09:43.311 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.316 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.319 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +07:09:43.329 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +07:09:43.335 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -22:37:04.057 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +07:09:43.335 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [1 items, 1,000.00 items/s, 1.00 ms/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 495.45M/15.28G/645.41M/1.14G/15.78G -22:37:04.058 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 164.86M/15.61G/120.35M/285.21M/15.78G +07:09:43.338 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. notBestScoreCount=16.6667 % geneAmbiguityCount=33.3333 % found entry: query_index: 0 target_index: 1 @@ -5948,64 +6021,64 @@ multiplicity: 1 query_length: 35 -22:37:04.064 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.086 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.088 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.110 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.355 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.407 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.409 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.464 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -22:37:04.133 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.134 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.136 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.137 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. -22:37:04.140 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.140 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. -22:37:04.140 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.140 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.537 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.539 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.549 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.550 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.562 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.562 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.562 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.562 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -22:37:04.140 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.141 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.562 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.562 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 520.61M/15.26G/620.24M/1.14G/15.78G -22:37:04.142 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.144 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. -22:37:04.147 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.186 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.188 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.217 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 38.56M/15.74G/347.31M/385.88M/15.78G +07:09:43.564 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.566 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.577 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.635 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.636 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.683 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -22:37:04.239 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.241 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.738 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.739 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) -22:37:04.243 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.749 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. Found input file with 2 target(s) -22:37:04.244 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.751 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. ... max number of reads was 10 First pass: determine which reads should be kept in the merged alignment. Scanning align-105 Scanning align-106 Found 40 logical alignment entries. Prepare merged too many hits information. -22:37:04.247 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.247 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. -22:37:04.247 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.247 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.755 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.756 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.756 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.756 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -22:37:04.247 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.248 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.756 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.756 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 120.35M/15.66G/215.20M/335.54M/15.78G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 66.10M/15.71G/319.78M/385.88M/15.78G Second pass: writing the merged alignment. -22:37:04.249 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.251 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. +07:09:43.758 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.759 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-106.tmh has no 'too many hits' information (test-results/alignments/merge/align-106.tmh does not exist). Assuming no queries have too many hits. Wrote 20 skipped: 20 50.000000% too many hits 0.000000% notBestScore: 50.000000% Total logical entries written: 20 Total bytes written: 0 @@ -6015,25 +6088,25 @@ Number of queries: 10 Number of targets: 4 Percent aligned: 100.0 -22:37:04.255 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.278 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.279 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.301 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.783 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.830 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.831 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.886 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -22:37:04.323 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.324 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.326 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.327 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. -22:37:04.327 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.942 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.943 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.949 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.959 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.960 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -22:37:04.327 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +07:09:43.960 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [1 items, 1,000.00 items/s, 1.00 ms/item] +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 145.51M/15.63G/190.03M/335.54M/15.78G -22:37:04.329 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 91.26M/15.69G/294.61M/385.88M/15.78G +07:09:43.962 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-105.tmh has no 'too many hits' information (test-results/alignments/merge/align-105.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1 position: 11 @@ -6114,19 +6187,19 @@ multiplicity: 1 query_length: 35 -22:37:04.333 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.356 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.357 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.379 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:43.974 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.025 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.027 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.082 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -22:37:04.401 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.402 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.161 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.162 WARN MessageChunksWriter - Using chunk-size=1000 [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 204.23M/15.57G/131.31M/335.54M/15.78G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 147.57M/15.63G/238.30M/385.88M/15.78G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -6255,30 +6328,30 @@ multiplicity: 1 query_length: 35 -22:37:04.464 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.487 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.488 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.510 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.326 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.374 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.375 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.422 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -22:37:04.532 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.533 WARN MessageChunksWriter - Using chunk-size=1000 -22:37:04.536 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:04.539 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:04.571 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:04.571 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:04.571 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:04.571 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:44.469 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.470 WARN MessageChunksWriter - Using chunk-size=1000 +07:09:44.478 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:44.485 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:44.530 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:44.530 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:44.530 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:44.530 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -22:37:04.571 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:04.572 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:44.530 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:44.530 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 110.07M/15.67G/225.47M/335.54M/15.78G -22:37:04.574 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. -22:37:04.585 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 239.84M/15.54G/146.04M/385.88M/15.78G +07:09:44.537 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +07:09:44.585 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. found entry: query_index: 0 target_index: 1999 position: 19991 @@ -6465,8 +6538,8 @@ fragment_index: 0 ambiguity: 1 -22:37:04.642 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 -22:37:04.642 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds +07:09:44.710 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 +07:09:44.710 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds [ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits [ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0 decoding: 4 @@ -6673,7 +6746,7 @@ Annotations loaded Annotations loaded Annotations loaded -[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 82.609 s - in TestSuite +[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 179.318 s - in TestSuite [INFO] [INFO] Results: [INFO] @@ -6682,14 +6755,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.041 s] -[INFO] Goby I/O ........................................... SUCCESS [ 7.290 s] -[INFO] Goby Full Distribution ............................. SUCCESS [01:58 min] +[INFO] Goby Framework ..................................... SUCCESS [ 0.079 s] +[INFO] Goby I/O ........................................... SUCCESS [ 19.041 s] +[INFO] Goby Full Distribution ............................. SUCCESS [03:44 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 02:06 min -[INFO] Finished at: 2025-02-05T22:38:34-12:00 +[INFO] Total time: 04:04 min +[INFO] Finished at: 2026-03-12T07:12:19+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -6760,14 +6833,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.395 s] -[INFO] Goby I/O ........................................... SUCCESS [ 0.059 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 0.038 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.788 s] +[INFO] Goby I/O ........................................... SUCCESS [ 0.215 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 0.166 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.635 s -[INFO] Finished at: 2025-02-05T22:38:36-12:00 +[INFO] Total time: 1.615 s +[INFO] Finished at: 2026-03-12T07:12:25+14:00 [INFO] ------------------------------------------------------------------------ mh_resolve_dependencies --non-interactive --offline --build -plibgoby-io-java --base-directory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 --non-explore Analysing pom.xml... @@ -6778,12 +6851,12 @@ > dpkg --search /usr/share/maven-repo/org/rosuda/REngine/REngine/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/rosuda/REngine/REngine -Feb 05, 2025 10:38:42 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Mar 12, 2026 7:12:34 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian > dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* dpkg failed to execute successfully Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2 -Feb 05, 2025 10:38:47 PM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Mar 12, 2026 7:12:39 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian ERROR: goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian @@ -6811,10 +6884,10 @@ dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${java:Depends} unused, but is defined -dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${maven:Depends} used, but is not defined +dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined dpkg-gencontrol: warning: Recommends field of package goby-java: substitution variable ${maven:OptionalDepends} used, but is not defined dpkg-gencontrol: warning: package goby-java: substitution variable ${java:Depends} unused, but is defined dh_md5sums @@ -6828,12 +6901,14 @@ 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/3950228/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3950228/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/1220965 and its subdirectories -I: Current time: Wed Feb 5 22:38:59 -12 2025 -I: pbuilder-time-stamp: 1738838339 +I: removing directory /srv/workspace/pbuilder/3950228 and its subdirectories +I: Current time: Thu Mar 12 07:13:07 +14 2026 +I: pbuilder-time-stamp: 1773249187