Diff of the two buildlogs: -- --- b1/build.log 2025-08-31 13:33:46.378524704 +0000 +++ b2/build.log 2025-08-31 13:47:24.303601484 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Aug 31 01:29:00 -12 2025 -I: pbuilder-time-stamp: 1756646940 +I: Current time: Sun Oct 4 09:56:46 +14 2026 +I: pbuilder-time-stamp: 1791057406 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -40,53 +40,85 @@ 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/1358061/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1381621/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +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 Oct 3 19:57 /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/1381621/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1381621/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='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' - DISTRIBUTION='forky' - HOME='/root' - HOST_ARCH='amd64' + 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]="x86_64-pc-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=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='a92db412af704b6ba232bc76631d4f3d' - 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='1358061' - PS1='# ' - PS2='> ' + INVOCATION_ID=342e2d551a674265bdbe5f94d408f0ba + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-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=1381621 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.hDVMjt6K/pbuilderrc_mWNH --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hDVMjt6K/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-11.dsc' - SUDO_GID='110' - SUDO_HOME='/var/lib/jenkins' - SUDO_UID='105' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.hDVMjt6K/pbuilderrc_ZNy6 --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hDVMjt6K/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-11.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.41+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.41-1 (2025-08-12) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1358061/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1381621/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -663,7 +695,7 @@ Get: 459 http://deb.debian.org/debian forky/main amd64 r-base-core amd64 4.5.1-1 [28.7 MB] Get: 460 http://deb.debian.org/debian forky/main amd64 r-cran-rjava amd64 1.0-11-2 [713 kB] Get: 461 http://deb.debian.org/debian forky/main amd64 testng all 6.9.12-4 [795 kB] -Fetched 388 MB in 4s (95.0 MB/s) +Fetched 388 MB in 1min 13s (5294 kB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:amd64. (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 ... 19897 files and directories currently installed.) @@ -2171,8 +2203,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sun Aug 31 13:30:16 UTC 2025. -Universal Time is now: Sun Aug 31 13:30:16 UTC 2025. +Local time is now: Sat Oct 3 20:04:46 UTC 2026. +Universal Time is now: Sat Oct 3 20:04:46 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... @@ -2765,7 +2797,11 @@ 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/1381621/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1381621/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 @@ -2913,48 +2949,83 @@ [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist -[WARNING] import org.apache.commons.cli.*; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.REXP; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.RVector; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist -[WARNING] import org.apache.commons.cli.*; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol +[WARNING] private static Result evaluateFisherExpression(final Rengine rengine, [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist -[WARNING] import javax.xml.bind.annotation.XmlAccessType; +[WARNING] symbol: class Rengine +[WARNING] location: class FisherExact +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist -[WARNING] import javax.xml.bind.annotation.XmlAccessorType; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol +[WARNING] private Rengine rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol -[WARNING] @XmlAccessorType(XmlAccessType.FIELD) +[WARNING] symbol: class Rengine +[WARNING] location: class GobyRengine +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol +[WARNING] public Rengine getRengine() { [WARNING] ^ -[WARNING] symbol: class XmlAccessorType -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:22: error: package javax.xml.bind.annotation does not exist -[WARNING] import javax.xml.bind.annotation.XmlElement; +[WARNING] symbol: class Rengine +[WARNING] location: class GobyRengine +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:23: error: package javax.xml.bind.annotation does not exist -[WARNING] import javax.xml.bind.annotation.XmlElementWrapper; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:24: error: package javax.xml.bind.annotation does not exist -[WARNING] import javax.xml.bind.annotation.XmlRootElement; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol +[WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks { [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:32: error: cannot find symbol -[WARNING] @XmlRootElement(name = "info-output") +[WARNING] symbol: class RMainLoopCallbacks +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol +[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { [WARNING] ^ -[WARNING] symbol: class XmlRootElement -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:21: error: package javax.xml.bind.annotation does not exist -[WARNING] import javax.xml.bind.annotation.XmlAccessType; +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol +[WARNING] public void rBusy(final Rengine rengine, final int which) { [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist -[WARNING] import javax.xml.bind.annotation.XmlAccessorType; +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol +[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol -[WARNING] @XmlAccessorType(XmlAccessType.FIELD) +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol +[WARNING] public void rShowMessage(final Rengine rengine, final String message) { [WARNING] ^ -[WARNING] symbol: class XmlAccessorType +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol +[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol +[WARNING] public void rFlushConsole(final Rengine rengine) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol +[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol +[WARNING] public void rLoadHistory(final Rengine re, final String filename) { +[WARNING] ^ +[WARNING] symbol: class Rengine +[WARNING] location: class RConsoleMainLoopCallback [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.RMainLoopCallbacks; [WARNING] ^ @@ -3005,83 +3076,85 @@ [WARNING] ^ [WARNING] symbol: class Rengine [WARNING] location: class RLoggerMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:27: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.REXP; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:28: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.RVector; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/EstimatedDistribution.java:22: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:29: error: package org.rosuda.JRI does not exist +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:208: error: cannot find symbol -[WARNING] private static Result evaluateFisherExpression(final Rengine rengine, +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist +[WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class FisherExact -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:21: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.RMainLoopCallbacks; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist +[WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:22: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol +[WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol -[WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks { +[WARNING] symbol: class XmlAccessorType +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:22: error: package javax.xml.bind.annotation does not exist +[WARNING] import javax.xml.bind.annotation.XmlElement; [WARNING] ^ -[WARNING] symbol: class RMainLoopCallbacks -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:35: error: cannot find symbol -[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:23: error: package javax.xml.bind.annotation does not exist +[WARNING] import javax.xml.bind.annotation.XmlElementWrapper; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:50: error: cannot find symbol -[WARNING] public void rBusy(final Rengine rengine, final int which) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:24: error: package javax.xml.bind.annotation does not exist +[WARNING] import javax.xml.bind.annotation.XmlRootElement; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:70: error: cannot find symbol -[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.java:32: error: cannot find symbol +[WARNING] @XmlRootElement(name = "info-output") [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:81: error: cannot find symbol -[WARNING] public void rShowMessage(final Rengine rengine, final String message) { +[WARNING] symbol: class XmlRootElement +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:21: error: package javax.xml.bind.annotation does not exist +[WARNING] import javax.xml.bind.annotation.XmlAccessType; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol -[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist +[WARNING] import javax.xml.bind.annotation.XmlAccessorType; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol -[WARNING] public void rFlushConsole(final Rengine rengine) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol +[WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol -[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { +[WARNING] symbol: class XmlAccessorType +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol -[WARNING] public void rLoadHistory(final Rengine re, final String filename) { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist +[WARNING] import DistLib.hypergeometric; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:24: error: package org.rosuda.JRI does not exist +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:56: error: cannot find symbol -[WARNING] private Rengine rengine; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol +[WARNING] Rengine rEngine; [WARNING] ^ [WARNING] symbol: class Rengine -[WARNING] location: class GobyRengine -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/GobyRengine.java:127: error: cannot find symbol -[WARNING] public Rengine getRengine() { +[WARNING] location: class FisherExactRCalculator +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist +[WARNING] import org.rosuda.JRI.Rengine; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist +[WARNING] import edu.rit.pj.ParallelTeam; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist +[WARNING] import javax.xml.bind.JAXBContext; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist +[WARNING] import javax.xml.bind.JAXBException; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist +[WARNING] import javax.xml.bind.Unmarshaller; +[WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol +[WARNING] private ParallelTeam team; +[WARNING] ^ +[WARNING] symbol: class ParallelTeam +[WARNING] location: class StatsMode +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist +[WARNING] import edu.rit.pj.PJProperties; [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class GobyRengine [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java:23: error: package org.apache.commons.cli does not exist [WARNING] import org.apache.commons.cli.*; [WARNING] ^ @@ -3123,29 +3196,6 @@ [WARNING] ^ [WARNING] symbol: class ParallelRegion [WARNING] location: class CompactAlignmentToAnnotationCountsMode -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:32: error: package edu.rit.pj does not exist -[WARNING] import edu.rit.pj.ParallelTeam; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:43: error: package javax.xml.bind does not exist -[WARNING] import javax.xml.bind.JAXBContext; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:44: error: package javax.xml.bind does not exist -[WARNING] import javax.xml.bind.JAXBException; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:45: error: package javax.xml.bind does not exist -[WARNING] import javax.xml.bind.Unmarshaller; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/StatsMode.java:76: error: cannot find symbol -[WARNING] private ParallelTeam team; -[WARNING] ^ -[WARNING] symbol: class ParallelTeam -[WARNING] location: class StatsMode -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/TestRConnectionMode.java:25: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/FastaToCompactMode.java:23: error: package edu.rit.pj does not exist -[WARNING] import edu.rit.pj.PJProperties; -[WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:34: error: package javax.xml.bind does not exist [WARNING] import javax.xml.bind.JAXBContext; [WARNING] ^ @@ -3167,9 +3217,6 @@ [WARNING] ^ [WARNING] symbol: class JAXBException [WARNING] location: class MethylStatsMode -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java:23: error: package org.apache.commons.cli does not exist -[WARNING] import org.apache.commons.cli.*; -[WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:30: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.CommandLine; [WARNING] ^ @@ -3179,35 +3226,25 @@ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:32: error: package org.apache.commons.exec does not exist [WARNING] import org.apache.commons.exec.PumpStreamHandler; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; -[WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.java:42: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:26: error: package org.rosuda.JRI does not exist +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.java:45: error: package org.rosuda.JRI does not exist [WARNING] import org.rosuda.JRI.Rengine; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactRCalculator.java:68: error: cannot find symbol -[WARNING] Rengine rEngine; -[WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class FisherExactRCalculator -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java:21: error: package DistLib does not exist -[WARNING] import DistLib.hypergeometric; -[WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/stats/AnnotationAveragingWriter.java:39: error: package org.rosuda.JRI does not exist -[WARNING] import org.rosuda.JRI.Rengine; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist +[WARNING] import edu.rit.pj.IntegerForLoop; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist -[WARNING] import org.apache.commons.cli.*; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist +[WARNING] import edu.rit.pj.ParallelRegion; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist -[WARNING] import org.apache.commons.cli.*; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:31: error: cannot find symbol +[WARNING] class BasenameParallelRegion extends ParallelRegion { [WARNING] ^ +[WARNING] symbol: class ParallelRegion [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/DoInParallel.java:21: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ @@ -3221,16 +3258,15 @@ [WARNING] ^ [WARNING] symbol: class ParallelTeam [WARNING] location: class DoInParallel -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist -[WARNING] import edu.rit.pj.IntegerForLoop; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java:22: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist -[WARNING] import edu.rit.pj.ParallelRegion; +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:31: error: cannot find symbol -[WARNING] class BasenameParallelRegion extends ParallelRegion { +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; [WARNING] ^ -[WARNING] symbol: class ParallelRegion [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ @@ -3588,9 +3624,6 @@ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/vcf/VCFParser.java:179: warning: invalid input: '<' [WARNING] * Set to <= 0 to scan the entire file. This must be set before calling readHeader() for the value to be used. [WARNING] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore -[WARNING] * Dequeues a document from the queue, returning an instance of {@link -[WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ @@ -3600,6 +3633,9 @@ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore [WARNING] * Dequeues a document from the queue, returning an instance of {@link [WARNING] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore +[WARNING] * Dequeues a document from the queue, returning an instance of {@link +[WARNING] ^ [WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/AlignedCountNormalization.java:73: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. [WARNING] public double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, [WARNING] ^ @@ -3643,14 +3679,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.046 s] -[INFO] Goby I/O ........................................... SUCCESS [ 15.346 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 19.246 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.092 s] +[INFO] Goby I/O ........................................... SUCCESS [01:01 min] +[INFO] Goby Full Distribution ............................. SUCCESS [ 34.632 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 34.742 s -[INFO] Finished at: 2025-08-31T01:31:18-12:00 +[INFO] Total time: 01:38 min +[INFO] Finished at: 2026-10-04T10:07:49+14:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' @@ -3809,1749 +3845,55 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite -SLF4J: Class path contains multiple SLF4J bindings. -SLF4J: Found binding in [jar:file:/usr/share/java/slf4j-simple.jar!/org/slf4j/impl/StaticLoggerBinder.class] -SLF4J: Found binding in [jar:file:/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven-repo/ch/qos/logback/logback-classic/debian/logback-classic-debian.jar!/org/slf4j/impl/StaticLoggerBinder.class] -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] -01:31:32.974 WARN MessageChunksWriter - Using chunk-size=10000 -Total logical entries written: 4 -Total bytes written: 0 -Average bytes/logical entry: 0.0 -Min query index: 1 -Max query index: 1 -Number of queries: 1 -Number of targets: 2 -Total logical entries written: 4 -Total bytes written: 62 -Average bytes/logical entry: 15.5 -Min query index: 1 -Max query index: 1 -Number of queries: 1 -Number of targets: 2 -01:31:33.041 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. -Annotations loaded -Annotations loaded -Annotations loaded -Annotations loaded -Annotations loaded -[main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 -count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} -count keys [0, 3, 5, 11, 13] --1 0.0 -0 0.0 -1 0.0 -2 0.0 -3 0.0 -4 0.0 -5 0.0 -6 0.0 -7 0.0 -8 0.0 -9 0.0 -10 0.0 -11 0.0 -12 0.0 -13 0.0 -14 0.0 -15 0.0 -16 0.0 -17 0.0 -18 0.0 -19 0.0 -20 0.0 -21 0.0 -22 0.0 -23 0.0 -24 0.0 -25 0.0 -26 0.0 -27 0.0 -28 0.0 -29 0.0 -30 0.0 -overlapping count 3, 4 0.0 -overlapping count 15, 17 0.0 -overlapping count 9, 18 2.0 -overlapping count 3, 8 2.0 -overlapping count 11, 12 0.0 -overlapping count 9, 10 1.0 -overlapping count 8, 9 0.0 -overlapping count 8, 8 0.0 -overlapping count 5, 6 0.0 -overlapping count 3, 3 0.0 -overlapping count 3, 12 5.0 -overlapping count -1, 2 0.0 -overlapping count 0, 45 6.0 -overlapping count 13, 15 0.0 --1 0.0 -0 0.0 -1 0.0 -2 0.0 -3 2.0 -4 2.0 -5 3.0 -6 3.0 -7 3.0 -8 3.0 -9 3.0 -10 3.0 -11 2.0 -12 2.0 -13 0.0 -14 0.0 -15 1.0 -16 1.0 -17 1.0 -18 1.0 -19 0.0 -20 0.0 -21 0.0 -22 0.0 -23 0.0 -24 0.0 -25 0.0 -26 0.0 -27 0.0 -28 0.0 -29 0.0 -30 0.0 -overlapping count 3, 4 2.0 -overlapping count 2, 3 2.0 -overlapping count 3, 8 4.0 -overlapping count 11, 12 2.0 -overlapping count 9, 10 3.0 -overlapping count 8, 9 4.0 -overlapping count 8, 8 3.0 -overlapping count 5, 6 3.0 -overlapping count 3, 3 2.0 -overlapping count 3, 12 5.0 -overlapping count -1, 2 0.0 -overlapping count 0, 45 6.0 -overlapping count 13, 15 1.0 -[ {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 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 1 -decoding: 2 -decoding: 3 -decoding: 4 -decoding: 3 -decoding: 1 -decoding: 2 -decoding: 1 -decoding: 2 -decoding: 3 -decoding: 1 -decoding: 2 -decoding: 1 -decoding: 2 -decoding: 1 -[ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits -[ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0 - {1} {0}decoding: 4 - {0} {0}decoding: 4 - {0} {0}decoding: 4 - {0}decoding: 4 - {0}decoding: 4 - {0}decoding: 4 -decoding: 4 - {0}decoding: 4 - {0}decoding: 4 -decoding: 4 - {0}decoding: 4 -decoding: 4 - {0}decoding: 4 -decoding: 4 - {0} {0} {0} {0} {0}decoding: 1 - {0} {0} {0} {0}decoding: 2 - {0} {0} {0} {0} {0}decoding: 3 -decoding: 4 - {0} {0} {0} {0}decoding: 3 - {0} {0} {0}decoding: 1 - {0} {0} {0} {0}decoding: 2 - {0} {0} {0}decoding: 1 - {0} {0} {0}decoding: 2 - {0} {0} {0} {0}decoding: 3 - {0} {0} {0}decoding: 1 - {0} {0} {0}decoding: 2 - {0} {0}decoding: 1 - {0} {0} {0}decoding: 2 - {0} {0}decoding: 1 -[ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits -[ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 4 -decoding: 1 -decoding: 2 -decoding: 3 -decoding: 4 -decoding: 3 -decoding: 1 -decoding: 2 -decoding: 1 -decoding: 2 -decoding: 3 -decoding: 1 -decoding: 2 -decoding: 1 -decoding: 2 -decoding: 1 -Total logical entries written: 1 -Total bytes written: 0 -Average bytes/logical entry: 0.0 -Min query index: 0 -Max query index: 0 -Number of queries: 1 -Number of targets: 45 -field CHROM value: 0 -field POS value: 145497099 -field ID value: . -field REF value: A -field ALT value: G -field QUAL value: 17.1 -field FILTER value: . -field INFO[DP] value: 2 -field INFO[DP4] value: 0,0,2,0 -field INFO[MQ] value: 25 -field INFO[FQ] value: -30.8 -field INFO[AF1] value: 0.9999 -field INFO[CI95] value: 0.5,1 -field INFO[PV4] value: -field INFO[INDEL] value: INDEL -field INFO[PC2] value: 3,3 -field INFO[PCHI2] value: 0.752 -field INFO[QCHI2] value: 1 -field INFO[RP] value: -field FORMAT[GT] value: -field FORMAT[GQ] value: -field FORMAT[GL] value: -field FORMAT[DP] value: -field FORMAT[SP] value: -field FORMAT[PL] value: -field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1 -field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42 -field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: -field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: -field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: -field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0 -field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1 -field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42 -field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: -field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: -field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: -field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0 -field CHROM gfi:0 value: 0 -field POS gfi:1 value: 145497099 -field ID gfi:2 value: . -field REF gfi:3 value: A -field ALT gfi:4 value: G -field QUAL gfi:5 value: 17.1 -field FILTER gfi:6 value: . -field FORMAT[GT] gfi:7 value: -field FORMAT[GQ] gfi:8 value: -field FORMAT[GL] gfi:9 value: -field FORMAT[DP] gfi:10 value: -field FORMAT[SP] gfi:11 value: -field FORMAT[PL] gfi:12 value: -field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1 -field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11 -field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: -field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: -field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: -field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0 -field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1 -field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42 -field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: -field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: -field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: -field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0 - peak : start :5 count :13 length :100010 - peak : start :100020 count :10 length :1 -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=6 count=1 -(0,1) -loading transition for reader[0] position=1 length=3 count=3 -(0,1)(1,4) -loading transition for reader[0] position=4 length=2 count=0 -(0,1)(1,4)(4,1) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=4 count=0 -(0,0) -loading transition for reader[0] position=1 length=1 count=1 -(0,0)(1,1) -loading transition for reader[0] position=2 length=4 count=0 -(0,0)(1,1)(2,0) -loading transition for reader[1] position=4 length=10 count=1 -(0,0)(1,1)(2,0)(4,1) -loading transition for reader[0] position=6 length=2 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2) -loading transition for reader[0] position=8 length=1 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1) -loading transition for reader[0] position=9 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) -loading transition for reader[0] position=10 length=2 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) -loading transition for reader[0] position=12 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) -loading transition for reader[0] position=13 length=3 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) -loading transition for reader[0] position=16 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=4 count=0 -loading transition for reader[0] position=1 length=1 count=1 -loading transition for reader[0] position=2 length=4 count=0 -loading transition for reader[1] position=4 length=10 count=1 -loading transition for reader[0] position=6 length=2 count=1 -loading transition for reader[0] position=8 length=1 count=0 -loading transition for reader[0] position=9 length=1 count=1 -loading transition for reader[0] position=10 length=2 count=0 -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 - appending (count=10,length=4) - appending (count=1,length=0) - appending (count=2,length=8) -Hello - appending (count=10,length=4) -01:32:16.787 WARN WiggleWindow - Not writing 101 7 -01:32:16.787 WARN WiggleWindow - Not writing 111 7 -01:32:16.787 WARN WiggleWindow - Not writing 131 8 -01:32:16.787 WARN WiggleWindow - Not writing 141 8 -01:32:16.787 WARN WiggleWindow - Not writing 151 8 - appending (count=0,length=1) - appending (count=4,length=3) - appending (count=1,length=3) - appending (count=0,length=2) - appending (count=3,length=1) - appending (count=1,length=1) - appending (count=0,length=1) - appending (count=4,length=3) - appending (count=0,length=5) - appending (count=3,length=1) - appending (count=0,length=2) - appending (count=2,length=1) - appending (count=0,length=2) - appending (count=3,length=1) - appending (count=2,length=1) - appending (count=0,length=1) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=6 count=1 -(0,1) -loading transition for reader[0] position=1 length=3 count=3 -(0,1)(1,4) -loading transition for reader[0] position=4 length=2 count=0 -(0,1)(1,4)(4,1) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=4 count=0 -(0,0) -loading transition for reader[0] position=1 length=1 count=1 -(0,0)(1,1) -loading transition for reader[0] position=2 length=4 count=0 -(0,0)(1,1)(2,0) -loading transition for reader[1] position=4 length=10 count=1 -(0,0)(1,1)(2,0)(4,1) -loading transition for reader[0] position=6 length=2 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2) -loading transition for reader[0] position=8 length=1 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1) -loading transition for reader[0] position=9 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) -loading transition for reader[0] position=10 length=2 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) -loading transition for reader[0] position=12 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) -loading transition for reader[0] position=13 length=3 count=0 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) -loading transition for reader[0] position=16 length=1 count=1 -(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) -loading transition for reader[0] position=0 length=1 count=0 -loading transition for reader[1] position=0 length=4 count=0 -loading transition for reader[0] position=1 length=1 count=1 -loading transition for reader[0] position=2 length=4 count=0 -loading transition for reader[1] position=4 length=10 count=1 -loading transition for reader[0] position=6 length=2 count=1 -loading transition for reader[0] position=8 length=1 count=0 -loading transition for reader[0] position=9 length=1 count=1 -loading transition for reader[0] position=10 length=2 count=0 -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 -loading transition for reader[0] position=0 length=1 count=0 -(0,0) -loading transition for reader[0] position=1 length=3 count=1 -(0,0)(1,1) -Appending count: 5827 length: 3 -Appending count: 12508 length: 8 -Appending count: 15206 length: 7 -Appending count: 44425 length: 6 -Appending count: 31128 length: 3 -Appending count: 48344 length: 6 -Appending count: 21874 length: 8 -Appending count: 27648 length: 10 -Appending count: 18572 length: 8 -Appending count: 33022 length: 7 -Appending count: 30052 length: 2 -Appending count: 49471 length: 7 -Appending count: 31867 length: 10 -Appending count: 41951 length: 8 -Appending count: 39724 length: 2 -Appending count: 11641 length: 2 -Appending count: 19178 length: 9 -Appending count: 28521 length: 4 -Appending count: 10517 length: 5 -Appending count: 32726 length: 8 -Appending count: 9384 length: 7 -Appending count: 28246 length: 6 -Appending count: 40818 length: 2 -Appending count: 35933 length: 5 -Appending count: 37006 length: 6 -Appending count: 1846 length: 10 -Appending count: 26882 length: 9 -Appending count: 36364 length: 3 -Appending count: 13921 length: 6 -Appending count: 48229 length: 9 - position= 0 count= 5827 - position= 1 count= 5827 - position= 2 count= 5827 - position= 3 count= 12508 - position= 4 count= 12508 - position= 5 count= 12508 - position= 6 count= 12508 - position= 7 count= 12508 - position= 8 count= 12508 - position= 9 count= 12508 - position= 10 count= 12508 - position= 11 count= 15206 - position= 12 count= 15206 - position= 13 count= 15206 - position= 14 count= 15206 - position= 15 count= 15206 - position= 16 count= 15206 - position= 17 count= 15206 - position= 18 count= 44425 - position= 19 count= 44425 - position= 20 count= 44425 - position= 21 count= 44425 - position= 22 count= 44425 - position= 23 count= 44425 - position= 24 count= 31128 - position= 25 count= 31128 - position= 26 count= 31128 - position= 27 count= 48344 - position= 28 count= 48344 - position= 29 count= 48344 - position= 30 count= 48344 - position= 31 count= 48344 - position= 32 count= 48344 - position= 33 count= 21874 - position= 34 count= 21874 - position= 35 count= 21874 - position= 36 count= 21874 - position= 37 count= 21874 - position= 38 count= 21874 - position= 39 count= 21874 - position= 40 count= 21874 - position= 41 count= 27648 - position= 42 count= 27648 - position= 43 count= 27648 - position= 44 count= 27648 - position= 45 count= 27648 - position= 46 count= 27648 - position= 47 count= 27648 - position= 48 count= 27648 - position= 49 count= 27648 - position= 50 count= 27648 - position= 51 count= 18572 - position= 52 count= 18572 - position= 53 count= 18572 - position= 54 count= 18572 - position= 55 count= 18572 - position= 56 count= 18572 - position= 57 count= 18572 - position= 58 count= 18572 - position= 59 count= 33022 - position= 60 count= 33022 - position= 61 count= 33022 - position= 62 count= 33022 - position= 63 count= 33022 - position= 64 count= 33022 - position= 65 count= 33022 - position= 66 count= 30052 - position= 67 count= 30052 - position= 68 count= 49471 - position= 69 count= 49471 - position= 70 count= 49471 - position= 71 count= 49471 - position= 72 count= 49471 - position= 73 count= 49471 - position= 74 count= 49471 - position= 75 count= 31867 - position= 76 count= 31867 - position= 77 count= 31867 - position= 78 count= 31867 - position= 79 count= 31867 - position= 80 count= 31867 - position= 81 count= 31867 - position= 82 count= 31867 - position= 83 count= 31867 - position= 84 count= 31867 - position= 85 count= 41951 - position= 86 count= 41951 - position= 87 count= 41951 - position= 88 count= 41951 - position= 89 count= 41951 - position= 90 count= 41951 - position= 91 count= 41951 - position= 92 count= 41951 - position= 93 count= 39724 - position= 94 count= 39724 - position= 95 count= 11641 - position= 96 count= 11641 - position= 97 count= 19178 - position= 98 count= 19178 - position= 99 count= 19178 - position= 100 count= 19178 - position= 101 count= 19178 - position= 102 count= 19178 - position= 103 count= 19178 - position= 104 count= 19178 - position= 105 count= 19178 - position= 106 count= 28521 - position= 107 count= 28521 - position= 108 count= 28521 - position= 109 count= 28521 - position= 110 count= 10517 - position= 111 count= 10517 - position= 112 count= 10517 - position= 113 count= 10517 - position= 114 count= 10517 - position= 115 count= 32726 - position= 116 count= 32726 - position= 117 count= 32726 - position= 118 count= 32726 - position= 119 count= 32726 - position= 120 count= 32726 - position= 121 count= 32726 - position= 122 count= 32726 - position= 123 count= 9384 - position= 124 count= 9384 - position= 125 count= 9384 - position= 126 count= 9384 - position= 127 count= 9384 - position= 128 count= 9384 - position= 129 count= 9384 - position= 130 count= 28246 - position= 131 count= 28246 - position= 132 count= 28246 - position= 133 count= 28246 - position= 134 count= 28246 - position= 135 count= 28246 - position= 136 count= 40818 - position= 137 count= 40818 - position= 138 count= 35933 - position= 139 count= 35933 - position= 140 count= 35933 - position= 141 count= 35933 - position= 142 count= 35933 - position= 143 count= 37006 - position= 144 count= 37006 - position= 145 count= 37006 - position= 146 count= 37006 - position= 147 count= 37006 - position= 148 count= 37006 - position= 149 count= 1846 - position= 150 count= 1846 - position= 151 count= 1846 - position= 152 count= 1846 - position= 153 count= 1846 - position= 154 count= 1846 - position= 155 count= 1846 - position= 156 count= 1846 - position= 157 count= 1846 - position= 158 count= 1846 - position= 159 count= 26882 - position= 160 count= 26882 - position= 161 count= 26882 - position= 162 count= 26882 - position= 163 count= 26882 - position= 164 count= 26882 - position= 165 count= 26882 - position= 166 count= 26882 - position= 167 count= 26882 - position= 168 count= 36364 - position= 169 count= 36364 - position= 170 count= 36364 - position= 171 count= 13921 - position= 172 count= 13921 - position= 173 count= 13921 - position= 174 count= 13921 - position= 175 count= 13921 - position= 176 count= 13921 - position= 177 count= 48229 - position= 178 count= 48229 - position= 179 count= 48229 - position= 180 count= 48229 - position= 181 count= 48229 - position= 182 count= 48229 - position= 183 count= 48229 - position= 184 count= 48229 - position= 185 count= 48229 -01:32:16.828 WARN MessageChunksWriter - Using chunk-size=9 -01:32:16.872 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 -01:32:16.876 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 -01:32:16.880 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 - 0 -AAC 3 -ACC 6 -ATC 9 -AGC 12 -AAC 15 -ACC 18 -ATC 21 -AGC 24 -AAC 27 -ACC 30 -ATC 33 -AGC 36 -AAC 39 -ACC 42 -ATC 45 -AGC 48 -AAC 51 -ACC 54 -ATC 57 -AGC 60 -AAC 63 -ACC 66 -ATC 69 -AGC 72 -AAC 75 -ACC 78 -ATC 81 -AGC>1 -NNTGAATGAGACCTA - -qPhred=1 -qPhred=2 -qPhred=3 -qPhred=4 -qPhred=5 -qPhred=6 -qPhred=7 -qPhred=8 -qPhred=9 -qPhred=10 -qPhred=11 -qPhred=12 -qPhred=13 -qPhred=14 -qPhred=15 -qPhred=16 -qPhred=17 -qPhred=18 -qPhred=19 -qPhred=20 -qPhred=21 -qPhred=22 -qPhred=23 -qPhred=24 -qPhred=25 -qPhred=26 -qPhred=27 -qPhred=28 -qPhred=29 -qPhred=30 -qPhred=31 -qPhred=32 -qPhred=33 -qPhred=34 -qPhred=35 -qPhred=36 -qPhred=37 -qPhred=38 -qPhred=39 -qPhred=40 -qPhred=41 -qPhred=42 -qPhred=43 -qPhred=44 -qPhred=45 -qPhred=46 -qPhred=47 -qPhred=48 -qPhred=49 -qPhred=50 -qPhred=51 -qPhred=52 -qPhred=53 -qPhred=54 -qPhred=55 -qPhred=56 -qPhred=57 -qPhred=58 -qPhred=59 -qPhred=60 -qPhred=61 -01:32:21.552 INFO RLoggerMainLoopCallback - +10:08:16.610 INFO RLoggerMainLoopCallback - -01:32:21.552 INFO RLoggerMainLoopCallback - R version 4.5.1 (2025-06-13) -- "Great Square Root" +10:08:16.616 INFO RLoggerMainLoopCallback - R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu -01:32:21.552 INFO RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY. +10:08:16.616 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. -01:32:21.552 INFO RLoggerMainLoopCallback - R is a collaborative project with many contributors. +10:08:16.617 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. -01:32:21.552 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or +10:08:16.617 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. -Processing test-data/sample-qual-scores/30reads.fa -Processed 0 read entries. -Min quality score: 2147483647 -Max quality score: -2147483648 -Avg quality score: 0 -Probable quality encoding scheme: fasta -Processing test-data/sample-qual-scores/30reads.fq -Processed 30 read entries. -Min quality score: 69 -Max quality score: 98 -Avg quality score: 94 -Probable quality encoding scheme: Illumina/Solexa -Loading test-data/fdr-mode/file1.vcf -Loading test-data/fdr-mode/file2.vcf -Loading test-data/fdr-mode/file3.vcf -adjusting column: PCHI2 -Combining test-data/fdr-mode/file1.vcf -Combining test-data/fdr-mode/file2.vcf -Combining test-data/fdr-mode/file3.vcf -Loading test-data/fdr-mode/file-B-1.vcf -Loading test-data/fdr-mode/file-B-2.vcf -adjusting column: PCHI2 -Combining test-data/fdr-mode/file-B-1.vcf -Combining test-data/fdr-mode/file-B-2.vcf -Loading test-data/fdr-mode/file-B-1.vcf -Loading test-data/fdr-mode/file-B-2.vcf -adjusting column: PCHI2 -Combining test-data/fdr-mode/file-B-1.vcf -Combining test-data/fdr-mode/file-B-2.vcf -Loading test-data/fdr-mode/file1.vcf -Loading test-data/fdr-mode/file2.vcf -Loading test-data/fdr-mode/file3.vcf -Combining test-data/fdr-mode/file1.vcf -Combining test-data/fdr-mode/file2.vcf -Combining test-data/fdr-mode/file3.vcf -Associating basename: basen0 to group: A -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:22.630 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 -01:32:22.633 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 -01:32:22.634 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 -01:32:22.636 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 -01:32:22.637 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 -01:32:22.638 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 -01:32:22.640 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 -01:32:22.642 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 -01:32:22.643 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 -01:32:22.645 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:22.777 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 -01:32:22.779 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 -01:32:22.780 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 -01:32:22.782 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 -01:32:22.783 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 -01:32:22.784 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 -01:32:22.786 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 -01:32:22.787 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 -01:32:22.788 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 -01:32:22.790 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:22.846 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 -01:32:22.847 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 -01:32:22.848 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 -01:32:22.849 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 -01:32:22.850 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 -01:32:22.852 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 -01:32:22.853 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 -01:32:22.854 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 -01:32:22.856 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 -01:32:22.857 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:22.909 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 -01:32:22.910 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 -01:32:22.911 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 -01:32:22.912 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 -01:32:22.914 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 -01:32:22.915 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 -01:32:22.916 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 -01:32:22.918 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 -01:32:22.919 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 -01:32:22.920 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:22.993 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 -01:32:22.994 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 -01:32:22.995 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 -01:32:22.996 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 -01:32:22.997 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 -01:32:22.998 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 -01:32:23.000 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 -01:32:23.001 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 -01:32:23.002 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 -01:32:23.003 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:23.048 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 -01:32:23.049 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 -01:32:23.051 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 -01:32:23.052 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 -01:32:23.053 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 -01:32:23.054 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 -01:32:23.055 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 -01:32:23.056 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 -01:32:23.057 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 -01:32:23.058 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:23.102 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 -01:32:23.103 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 -01:32:23.104 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 -01:32:23.106 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 -01:32:23.107 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 -01:32:23.108 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 -01:32:23.109 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 -01:32:23.110 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 -01:32:23.111 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 -01:32:23.112 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:23.157 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 -01:32:23.158 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 -01:32:23.159 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 -01:32:23.160 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 -01:32:23.161 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 -01:32:23.162 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 -01:32:23.163 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 -01:32:23.164 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 -01:32:23.165 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 -01:32:23.167 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:23.212 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 -01:32:23.213 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 -01:32:23.214 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 -01:32:23.215 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 -01:32:23.216 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 -01:32:23.217 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 -01:32:23.218 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 -01:32:23.219 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 -01:32:23.220 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 -01:32:23.221 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:23.265 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 -01:32:23.266 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 -01:32:23.267 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 -01:32:23.268 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 -01:32:23.269 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 -01:32:23.270 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 -01:32:23.271 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 -01:32:23.272 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 -01:32:23.273 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 -01:32:23.274 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -Comparing A/B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Filtering reads that have these criteria: -q<30 -#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 -01:32:23.339 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 -01:32:23.340 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 -01:32:23.341 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 -01:32:23.342 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 -01:32:23.343 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 -01:32:23.344 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 -01:32:23.345 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 -01:32:23.346 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 -01:32:23.347 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 -01:32:23.348 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 -Associating basename: basen1 to group: A -Associating basename: basen2 to group: A -Associating basename: basen3 to group: A -Associating basename: basen4 to group: A -Associating basename: basen5 to group: B -Associating basename: basen6 to group: B -Associating basename: basen7 to group: B -Associating basename: basen8 to group: B -Associating basename: basen9 to group: B -sample: basen0 group A -sample: basen2 group A -sample: basen4 group A -sample: basen3 group A -sample: basen1 group A -sample: basen9 group B -sample: basen6 group B -sample: basen5 group B -sample: basen7 group B -sample: basen8 group B -Using processor NONE -Methylation format ignores thresholdDistinctReadIndices. Additionally, the minimum coverage needed for a site to be reported can be changed with --minimum-variation-support. -Filtering reads that have these criteria: -[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 -01:32:23.399 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 -01:32:23.400 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 -01:32:23.401 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 -01:32:23.402 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 -01:32:23.403 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 -01:32:23.404 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 -01:32:23.405 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 -01:32:23.406 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 -01:32:23.407 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 -01:32:23.408 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 -info: + ref: A s=0 -info: + ref: A s=0 -info: + ref: A s=0 -info: + ref: A s=0 -info: + /T q=40 s=0 -info: - /T q=40 s=0 -info: + /C q=10 s=0 -info: + /C q=20 s=0 -info: + /C q=30 s=0 -info: + /C q=40 s=0 -info: + /C q=40 s=0 -info: + /C q=40 s=0 -info: + /C q=40 s=0 -info: + /C q=10 s=0 -info: + /C q=20 s=0 -info: + /N q=30 s=0 -info: + ref: A s=1 -info: + ref: A s=1 -info: + ref: A s=1 -info: + ref: A s=1 -info: + ref: A s=1 -info: + ref: A s=1 -info: + ref: A s=1 -info: + ref: A s=1 -info: + ref: A s=1 -info: + ref: A s=1 -info: + /T q=40 s=1 -info: + /T q=10 s=1 -info: + /T q=20 s=1 -info: + /T q=30 s=1 -info: + /N q=40 s=1 -info: + /N q=40 s=1 -list: pos=-1 #bases: 33 #indels: 0 -filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + /C q=10 s=0, + /C q=20 s=0, + /C q=30 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=10 s=0, + /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + /T q=40 s=1, + /T q=10 s=1, + /T q=20 s=1, + /T q=30 s=1, + /N q=40 s=1, + /N q=40 s=1} -Scanning target file.. -Target file had 1 entries. -Wrote 1 target ids to alignment header. -Setting quality threshold to 0.05 -Total logical entries written: 2 -Total bytes written: 0 -Average bytes/logical entry: 0.0 -Min query index: 0 -Max query index: 0 -Number of queries: 3 -Number of targets: 3 -Removed by quality filter: 0 -Not best score: 1 -Number of alignments written: 2 -query_index: 0 -target_index: 0 -position: 14977972 -score: 780.0 -matching_reverse_strand: false -multiplicity: 1 -number_of_mismatches: 1 -number_of_indels: 0 -query_length: 142 -query_aligned_length: 134 -target_aligned_length: 134 -sequence_variations { - to: "T" - from: "A" - position: 6 - to_quality: "/" - read_index: 14 -} -fragment_index: 0 -query_index_occurrences: 2 -ambiguity: 1 - -Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads -Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads -Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads -[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences - 1/1 ..T - -TTC[27]->CGT[27] / qual=1:2:3 -A[15]->G[20] / qual=20 -A[15]->G[20] / qual=20 -01:32:24.406 INFO BullardUpperQuartileNormalization - normalization denominator 52999.6 for sample B-7 -01:32:24.406 INFO BullardUpperQuartileNormalization - normalization denominator 51121.7 for sample B-3 -01:32:24.406 INFO BullardUpperQuartileNormalization - normalization denominator 102313 for sample A-3 -01:32:24.406 INFO BullardUpperQuartileNormalization - normalization denominator 102939 for sample A-12 -01:32:24.406 INFO BullardUpperQuartileNormalization - normalization denominator 52512.7 for sample B-15 -01:32:24.406 INFO BullardUpperQuartileNormalization - normalization denominator 52443.2 for sample B-14 -01:32:24.406 INFO BullardUpperQuartileNormalization - normalization denominator 52443.2 for sample B-11 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 105025 for sample A-17 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 50982.6 for sample B-2 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 53277.8 for sample B-10 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 102661 for sample A-16 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 52512.7 for sample B-8 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 52234.5 for sample B-4 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 107529 for sample A-2 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 106138 for sample A-0 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 53347.4 for sample B-6 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 103078 for sample A-9 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 104330 for sample A-8 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 101478 for sample A-5 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 102452 for sample A-4 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 106764 for sample A-6 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 107669 for sample A-7 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 52721.4 for sample B-5 -01:32:24.407 INFO BullardUpperQuartileNormalization - normalization denominator 100296 for sample A-10 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 101965 for sample A-14 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 53486.5 for sample B-9 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 105651 for sample A-1 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 51956.3 for sample B-0 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 52999.6 for sample B-12 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 53138.7 for sample B-13 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 105373 for sample A-19 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 105234 for sample A-18 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 102522 for sample A-15 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 53208.3 for sample B-1 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 103078 for sample A-13 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 106903 for sample A-11 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 51539.0 for sample B-16 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 51747.7 for sample B-17 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 51817.2 for sample B-19 -01:32:24.408 INFO BullardUpperQuartileNormalization - normalization denominator 52025.9 for sample B-18 -##fileformat=VCFv4.1 -##Goby=UNKNOWN -##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data, -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB - -01:32:24.455 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -01:32:24.487 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -01:32:24.488 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -01:32:24.500 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -01:32:24.500 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -01:32:24.604 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -01:32:24.637 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. -01:32:24.637 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -01:32:24.738 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -01:32:24.755 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] ] -[ 2 [2.576842E-5, 4.294736666666667E-4] ] -[ 3 [9.814783E-5, 9.471342857142858E-4] ] -[ 4 [1.05261E-4, 9.471342857142858E-4] ] -[ 5 [1.241481E-4, 9.471342857142858E-4] ] -[ 6 [1.325988E-4, 9.471342857142858E-4] ] -[ 7 [1.568503E-4, 9.803143750000002E-4] ] -[ 8 [2.254557E-4, 0.0012525316666666666] ] -[ 9 [3.79538E-4, 0.00189769] ] -[ 10 [6.114943E-4, 0.0027795195454545455] ] -[ 11 [0.001613954, 0.006724808333333334] ] -[ 12 [0.00330243, 0.012636935714285714] ] -[ 13 [0.003538342, 0.012636935714285714] ] -[ 14 [0.005236997, 0.017456656666666667] ] -[ 15 [0.006831909, 0.020762429411764708] ] -[ 16 [0.007059226, 0.020762429411764708] ] -[ 17 [0.008805129, 0.024458691666666667] ] -[ 18 [0.00940104, 0.02473957894736842] ] -[ 19 [0.01129798, 0.028244949999999998] ] -[ 20 [0.02115017, 0.050357547619047614] ] -[ 21 [0.04922736, 0.11188036363636364] ] -[ 22 [0.06053298, 0.1304633125] ] -[ 23 [0.06262239, 0.1304633125] ] -[ 24 [0.07395153, 0.14790306] ] -[ 25 [0.08281103, 0.15925198076923075] ] -[ 26 [0.08633331, 0.1598765] ] -[ 27 [0.1190654, 0.21261678571428572] ] -[ 28 [0.1890796, 0.32599931034482754] ] -[ 29 [0.2058494, 0.3430823333333333] ] -[ 30 [0.2209214, 0.3563248387096774] ] -[ 31 [0.2856, 0.44625000000000004] ] -[ 32 [0.3048895, 0.4619537878787878] ] -[ 33 [0.4660682, 0.6835770833333333] ] -[ 34 [0.4830809, 0.6835770833333333] ] -[ 35 [0.4921755, 0.6835770833333333] ] -[ 36 [0.5319453, 0.718845] ] -[ 37 [0.575155, 0.7414352564102564] ] -[ 38 [0.5783195, 0.7414352564102564] ] -[ 39 [0.6185894, 0.7626062790697675] ] -[ 40 [0.636362, 0.7626062790697675] ] -[ 41 [0.6448587, 0.7626062790697675] ] -[ 42 [0.6558414, 0.7626062790697675] ] -[ 43 [0.6885884, 0.7824868181818182] ] -[ 44 [0.7189864, 0.7988737777777778] ] -[ 45 [0.8179539, 0.8802645744680851] ] -[ 46 [0.8274487, 0.8802645744680851] ] -[ 47 [0.89713, 0.9304775510204082] ] -[ 48 [0.911868, 0.9304775510204082] ] -[ 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 [1.0032315810929742, 0.49824605517371273, 0.004654669090989201, -1.0050697122090833, 0.0, 0.0] ] - -truncated fdr=3.53108e-05 original=3.53108e-05 -truncated fdr=0.00128842 original=0.00128842 -truncated fdr=0.00128842 original=0.00128842 -truncated fdr=0.00284140 original=0.00284140 -truncated fdr=0.00284140 original=0.00284140 -truncated fdr=0.00284140 original=0.00284140 -truncated fdr=0.00284140 original=0.00284140 -truncated fdr=0.00294094 original=0.00294094 -truncated fdr=0.00375760 original=0.00375760 -truncated fdr=0.00569307 original=0.00569307 -truncated fdr=0.00833856 original=0.00833856 -truncated fdr=0.0201744 original=0.0201744 -truncated fdr=0.0379108 original=0.0379108 -truncated fdr=0.0379108 original=0.0379108 -truncated fdr=0.0523700 original=0.0523700 -truncated fdr=0.0622873 original=0.0622873 -truncated fdr=0.0622873 original=0.0622873 -truncated fdr=0.0733761 original=0.0733761 -truncated fdr=0.0742187 original=0.0742187 -truncated fdr=0.0847349 original=0.0847349 -truncated fdr=0.151073 original=0.151073 -truncated fdr=0.335641 original=0.335641 -truncated fdr=0.391390 original=0.391390 -truncated fdr=0.391390 original=0.391390 -truncated fdr=0.443709 original=0.443709 -truncated fdr=0.477756 original=0.477756 -truncated fdr=0.479630 original=0.479630 -truncated fdr=0.637850 original=0.637850 -truncated fdr=0.977998 original=0.977998 -truncated fdr=1.00000 original=1.00000 -truncated fdr=1.00000 original=1.00000 -truncated fdr=1.00000 original=1.00000 -truncated fdr=1.00000 original=1.00000 -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 40 threads. -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 40 threads. -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 40 threads. -[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 40 threads. -Creating base test directory: test-results/stats-writer -allele: A ref: [CC] alt: [T]Creating base test directory: test-results/stats -[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. -[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. -[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. -[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. -[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. -[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. -[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. -[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. -[main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression. -01:32:40.487 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:40.522 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:40.523 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:40.660 WARN MessageChunksWriter - Using chunk-size=1000 +SLF4J: Class path contains multiple SLF4J bindings. +SLF4J: Found binding in [jar:file:/usr/share/java/slf4j-simple.jar!/org/slf4j/impl/StaticLoggerBinder.class] +SLF4J: Found binding in [jar:file:/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven-repo/ch/qos/logback/logback-classic/debian/logback-classic-debian.jar!/org/slf4j/impl/StaticLoggerBinder.class] +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] +10:08:16.857 WARN MessageChunksWriter - Using chunk-size=10000 +10:08:17.050 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.129 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.133 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.170 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:32:40.686 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:40.687 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:40.694 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. -01:32:40.724 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. -01:32:40.724 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. +10:08:17.304 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.356 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.375 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. +10:08:17.386 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. +10:08:17.444 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. +10:08:17.444 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 -01:32:40.724 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. +10:08:17.445 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 [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: 2ms; used/avail/free/total/max mem: 157.50M/20.93G/178.04M/335.54M/21.09G -01:32:40.731 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: 7ms; used/avail/free/total/max mem: 47.28M/21.04G/1.29G/1.34G/21.09G +10:08:17.458 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 @@ -5632,36 +3974,36 @@ multiplicity: 1 query_length: 35 -01:32:40.766 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. -01:32:40.769 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. -01:32:40.800 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. -01:32:40.800 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. -01:32:40.800 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. -01:32:40.800 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. +10:08:17.580 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. +10:08:17.584 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. +10:08:17.635 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. +10:08:17.636 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. +10:08:17.636 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. +10:08:17.636 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 -01:32:40.800 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. -01:32:40.801 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. +10:08:17.636 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. +10:08:17.636 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: 41ms; used/avail/free/total/max mem: 207.85M/20.88G/127.69M/335.54M/21.09G -01:32:40.844 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. -01:32:40.858 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. -01:32:40.886 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:40.922 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:40.924 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:40.955 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 21ms; used/avail/free/total/max mem: 53.94M/21.04G/113.83M/167.77M/21.09G +10:08:17.661 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. +10:08:17.688 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. +10:08:17.744 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.775 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.778 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.809 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:32:41.030 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.031 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.840 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.842 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: 7ms [2 items, 333.33 items/s, 3.00 ms/item]; used/avail/free/total/max mem: 81.78M/21.01G/253.76M/335.54M/21.09G +[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: 30.33M/21.06G/154.22M/184.55M/21.09G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -5790,25 +4132,25 @@ multiplicity: 1 query_length: 35 -01:32:41.129 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.209 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.352 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.448 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.962 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.986 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:17.988 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.011 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:32:41.554 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.818 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.820 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. -01:32:41.826 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. -01:32:41.827 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. +10:08:18.035 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.036 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.039 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. +10:08:18.055 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. +10:08:18.055 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 -01:32:41.827 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. +10:08:18.055 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 - 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: 141.83M/20.95G/193.71M/335.54M/21.09G -01:32:41.829 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: 2ms; used/avail/free/total/max mem: 93.53M/21.00G/91.02M/184.55M/21.09G +10:08:18.059 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 @@ -5834,64 +4176,64 @@ multiplicity: 1 query_length: 35 -01:32:41.833 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.897 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.898 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.928 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.070 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.094 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.096 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.131 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:32:41.976 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.977 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:41.985 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. -01:32:41.986 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. -01:32:41.988 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. -01:32:41.988 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. -01:32:41.988 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. -01:32:41.988 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. +10:08:18.252 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.402 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.407 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. +10:08:18.409 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. +10:08:18.414 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. +10:08:18.414 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. +10:08:18.414 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. +10:08:18.414 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 -01:32:41.988 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. -01:32:41.988 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. +10:08:18.414 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. +10:08:18.414 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: 1ms [2 items, ? items/s, 0.00 ns/item] +[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 - 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: 168.73M/20.92G/166.82M/335.54M/21.09G -01:32:41.990 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. -01:32:41.991 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. -01:32:41.994 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.024 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.025 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.210 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 33.73M/21.06G/150.82M/184.55M/21.09G +10:08:18.419 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. +10:08:18.423 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. +10:08:18.431 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.464 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.467 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.502 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:32:42.446 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.447 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.536 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.538 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) -01:32:42.452 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. +10:08:18.543 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) -01:32:42.453 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. +10:08:18.546 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. -01:32:42.455 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. -01:32:42.455 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. -01:32:42.455 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. -01:32:42.455 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. +10:08:18.552 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. +10:08:18.552 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. +10:08:18.552 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. +10:08:18.552 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 -01:32:42.456 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. -01:32:42.456 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. +10:08:18.553 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. +10:08:18.553 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: 1ms [2 items, ? items/s, 0.00 ns/item] +[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 - 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: 191.97M/20.90G/143.57M/335.54M/21.09G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 60.13M/21.03G/124.42M/184.55M/21.09G Second pass: writing the merged alignment. -01:32:42.458 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. -01:32:42.459 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. +10:08:18.559 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. +10:08:18.562 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. Wrote 20 skipped: 20 50.000000% too many hits 0.000000% notBestScore: 50.000000% Total logical entries written: 20 Total bytes written: 0 @@ -5901,25 +4243,25 @@ Number of queries: 10 Number of targets: 4 Percent aligned: 100.0 -01:32:42.462 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.519 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.521 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.564 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.570 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.659 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.662 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.704 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:32:42.632 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.633 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.655 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. -01:32:42.656 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. -01:32:42.657 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. +10:08:18.737 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.738 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.741 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. +10:08:18.743 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. +10:08:18.743 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 -01:32:42.657 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. +10:08:18.743 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: 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: 219.06M/20.87G/116.49M/335.54M/21.09G -01:32:42.659 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: 10ms; used/avail/free/total/max mem: 85.64M/21.00G/98.91M/184.55M/21.09G +10:08:18.754 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 @@ -6000,19 +4342,19 @@ multiplicity: 1 query_length: 35 -01:32:42.662 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.749 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.750 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:42.772 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.764 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.810 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.812 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.853 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:32:42.913 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.061 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.876 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.877 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: 75.82M/21.01G/259.72M/335.54M/21.09G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 60.21M/21.03G/124.34M/184.55M/21.09G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -6141,30 +4483,30 @@ multiplicity: 1 query_length: 35 -01:32:43.295 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.319 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.321 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.343 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:18.973 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.082 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.084 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.109 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:32:43.368 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.369 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.372 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. -01:32:43.375 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. -01:32:43.398 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. -01:32:43.399 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. -01:32:43.399 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. -01:32:43.399 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. +10:08:19.135 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.137 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.142 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. +10:08:19.145 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. +10:08:19.175 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. +10:08:19.176 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. +10:08:19.176 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. +10:08:19.176 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 -01:32:43.399 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. -01:32:43.399 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. +10:08:19.176 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. +10:08:19.176 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: 166.49M/20.92G/169.06M/335.54M/21.09G -01:32:43.403 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. -01:32:43.414 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: 66.78M/21.02G/117.77M/184.55M/21.09G +10:08:19.179 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. +10:08:19.195 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 @@ -6325,7 +4667,7 @@ multiplicity: 1 query_length: 35 -01:32:43.452 WARN MessageChunksWriter - Using chunk-size=2 +10:08:19.350 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 0 Total bytes written: 31 Average bytes/logical entry: Infinity @@ -6334,7 +4676,7 @@ Number of queries: 2 Number of targets: 0 97 -01:32:43.457 WARN MessageChunksWriter - Using chunk-size=2 +10:08:19.359 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -6342,7 +4684,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.463 WARN MessageChunksWriter - Using chunk-size=2 +10:08:19.380 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -6350,7 +4692,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.465 WARN MessageChunksWriter - Using chunk-size=2 +10:08:19.383 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -6358,7 +4700,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.467 WARN MessageChunksWriter - Using chunk-size=2 +10:08:19.388 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -6366,69 +4708,34 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -read =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT -expected =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT -recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT -read =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG -expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -read =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG -expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -read =TAAAACCTAAAAAAAAAAAAAAACCCC -expected =TAAAA--TAAAAAAAAAAAAAAACCCC -recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC -read =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA -expected =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA -recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA -read =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG -expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG -read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT -expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT -recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT -01:32:43.489 WARN MessageChunksWriter - Using chunk-size=1000 +query_index: 0 +target_index: 0 +position: 0 +query_position: 0 +matching_reverse_strand: false +query_length: 75 +query_aligned_length: 75 +target_aligned_length: 75 +mapping_quality: 255 +pair_flags: 0 +fragment_index: 0 +ambiguity: 1 + +query_index: 1 +target_index: 0 +position: 1 +query_position: 0 +matching_reverse_strand: false +query_length: 75 +query_aligned_length: 75 +target_aligned_length: 75 +mapping_quality: 255 +pair_flags: 0 +fragment_index: 0 +ambiguity: 1 + +10:08:19.454 WARN MessageChunksWriter - Using chunk-size=1000 -Setting quality threshold to 0.02 -01:32:43.493 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.498 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 -01:32:43.504 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.506 WARN MessageChunksWriter - Using chunk-size=1000 -entry: score=30.0000 readOriginIndex=0 -entry: score=30.0000 readOriginIndex=0 -Scanned 2 entries -01:32:43.510 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.511 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.519 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.520 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.528 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.529 WARN MessageChunksWriter - Using chunk-size=1000 -0 -2 -01:32:43.534 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.536 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 -01:32:43.543 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.544 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.548 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.549 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.555 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.556 WARN MessageChunksWriter - Using chunk-size=1000 -entry: score=50.0000 readOriginIndex=3 -entry: score=50.0000 readOriginIndex=3 -entry: score=50.0000 readOriginIndex=3 -entry: score=30.0000 readOriginIndex=0 -entry: score=30.0000 readOriginIndex=0 -Scanned 5 entries entry:query_index: 0 target_index: 0 position: 5 @@ -6504,7 +4811,145 @@ read_index: 20 } -01:32:43.597 WARN MessageChunksWriter - Using chunk-size=2 +10:08:19.477 WARN MessageChunksWriter - Using chunk-size=1000 +Total logical entries written: 20000 +Total bytes written: 77210 +Average bytes/logical entry: 3.8605 +Min query index: 0 +Max query index: 1999 +Number of queries: 2000 +Number of targets: 10 +10:08:19.714 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.749 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 +10:08:19.759 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.760 WARN MessageChunksWriter - Using chunk-size=1000 +entry: score=30.0000 readOriginIndex=0 +entry: score=30.0000 readOriginIndex=0 +Scanned 2 entries +10:08:19.764 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.765 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.772 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.773 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.779 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.780 WARN MessageChunksWriter - Using chunk-size=1000 +0 +2 +10:08:19.787 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.789 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 +10:08:19.796 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.797 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.803 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.805 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.811 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.812 WARN MessageChunksWriter - Using chunk-size=1000 +entry: score=50.0000 readOriginIndex=3 +entry: score=50.0000 readOriginIndex=3 +entry: score=50.0000 readOriginIndex=3 +entry: score=30.0000 readOriginIndex=0 +entry: score=30.0000 readOriginIndex=0 +Scanned 5 entries +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' +Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1' +Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1' +Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2' +Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2' +Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2' +Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20' +Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20' +Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2' +Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2' +Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20' +Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)' +Processing queryIndex=0 with description '0 perfect match' +Processing queryIndex=1 with description '1 perfect match on reverse strand' +Processing queryIndex=2 with description '2 mutation' +Processing queryIndex=3 with description '3 mutation on reverse strand' +Processing queryIndex=4 with description '4 insertion' +Processing queryIndex=6 with description '6 deletion' +Processing queryIndex=7 with description '7 deletion on reverse strand' +Processing queryIndex=27 with description '27 padding left & right, deletion then mutation' +Processing queryIndex=24 with description '24 padding left & right, mutation, deletion' +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' +10:08:19.903 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.904 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.905 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.914 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.915 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.916 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.928 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.930 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.931 WARN MessageChunksWriter - Using chunk-size=1000 +entry.position(): 1 +entry.position(): 2 +entry.position(): 3 +entry.position(): 5 +entry.position(): 6 +entry.position(): 7 +entry.position(): 8 +entry.position(): 9 +entry.position(): 10 +entry.position(): 10 +entry.position(): 12 +entry.position(): 99 +10:08:19.941 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.947 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.950 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.959 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.960 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.962 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.965 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 +10:08:19.966 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 +10:08:19.968 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 +10:08:19.973 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.975 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.977 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:19.993 WARN MessageChunksWriter - Using chunk-size=1 +10:08:19.999 WARN MessageChunksWriter - Using chunk-size=1 +10:08:20.004 WARN MessageChunksWriter - Using chunk-size=1 +10:08:20.008 WARN MessageChunksWriter - Using chunk-size=1 +read =CTCCAGAACTGTAAGATAATAAGTTGGTGTTGTTTT +expected =TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT +recons. ref=TTCCAGAACTGTAAGATAATAAGTTTGTGTTGTTTT +read =TTTCCCACATTTCCCATCACCACTACTACGGATACAGAACGGGG +expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +read =TTTCCCAAATTTCACATCACTACTACACGGATACAGAACGGGG +expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +read =TAAAACCTAAAAAAAAAAAAAAACCCC +expected =TAAAA--TAAAAAAAAAAAAAAACCCC +recons. ref=TAAAA--TAAAAAAAAAAAAAAACCCC +read =TTTTGATGAAGTCTCTGTGTCCTGGGGCATCAATGATGGTCACA +expected =TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA +recons. ref=TTTTGACGAAGTCTCTATGTCCT-GGGCATCAATGATGGTCACA +read =TTTCCCAAATTTCACATCACTACACTACGGATACAGAACGGGG +expected =TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +recons. ref=TTTCCCAAATTTCACATCACTACTACTACGGATACAGAACGGGG +read =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTATCTTTTT +expected =CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT +recons. ref=CCATGACCAACATAACTGTGGTGTCATGCATTTGGTAT-TTTTAAT +[main] WARN org.campagnelab.goby.alignments.BufferedSortingAlignmentWriter - Local sorting strategy failed to restore sort order. The destination has been marked as unsorted. You must sort the output manually to improve compression. +10:08:20.043 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -6512,7 +4957,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.600 WARN MessageChunksWriter - Using chunk-size=2 +10:08:20.047 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -6520,7 +4965,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.606 WARN MessageChunksWriter - Using chunk-size=2 +10:08:20.050 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -6528,7 +4973,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.613 WARN MessageChunksWriter - Using chunk-size=2 +10:08:20.057 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -6536,7 +4981,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.623 WARN MessageChunksWriter - Using chunk-size=2 +10:08:20.070 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -6544,7 +4989,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.626 WARN MessageChunksWriter - Using chunk-size=2 +10:08:20.081 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -6552,7 +4997,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.636 WARN MessageChunksWriter - Using chunk-size=2 +10:08:20.100 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -6560,122 +5005,1702 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:32:43.647 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.649 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.650 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.658 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.659 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.661 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.670 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.671 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.674 WARN MessageChunksWriter - Using chunk-size=1000 -entry.position(): 1 -entry.position(): 2 -entry.position(): 3 -entry.position(): 5 -entry.position(): 6 -entry.position(): 7 -entry.position(): 8 -entry.position(): 9 -entry.position(): 10 -entry.position(): 10 -entry.position(): 12 -entry.position(): 99 -01:32:43.683 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.684 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.686 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.715 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.716 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.717 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.729 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 -01:32:43.730 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 -01:32:43.734 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 -01:32:43.740 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.747 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.748 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.770 WARN MessageChunksWriter - Using chunk-size=1 -01:32:43.777 WARN MessageChunksWriter - Using chunk-size=1 -01:32:43.781 WARN MessageChunksWriter - Using chunk-size=1 -01:32:43.785 WARN MessageChunksWriter - Using chunk-size=1 -01:32:43.793 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.796 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.804 WARN MessageChunksWriter - Using chunk-size=1000 -01:32:43.808 WARN MessageChunksWriter - Using chunk-size=1000 +Setting quality threshold to 0.02 +10:08:20.606 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:20.609 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:20.649 WARN MessageChunksWriter - Using chunk-size=1000 +10:08:20.652 WARN MessageChunksWriter - Using chunk-size=1000 0 23 +Total logical entries written: 4 +Total bytes written: 0 +Average bytes/logical entry: 0.0 +Min query index: 1 +Max query index: 1 +Number of queries: 1 +Number of targets: 2 +Total logical entries written: 4 +Total bytes written: 62 +Average bytes/logical entry: 15.5 +Min query index: 1 +Max query index: 1 +Number of queries: 1 +Number of targets: 2 +Annotations loaded +Annotations loaded +Annotations loaded +Annotations loaded +Annotations loaded +count perbase{0=>0, 13=>0, 11=>2, 3=>2, 5=>3} +count keys [0, 3, 5, 11, 13] +-1 0.0 +0 0.0 +1 0.0 +2 0.0 +3 0.0 +4 0.0 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +10 0.0 +11 0.0 +12 0.0 +13 0.0 +14 0.0 +15 0.0 +16 0.0 +17 0.0 +18 0.0 +19 0.0 +20 0.0 +21 0.0 +22 0.0 +23 0.0 +24 0.0 +25 0.0 +26 0.0 +27 0.0 +28 0.0 +29 0.0 +30 0.0 +overlapping count 3, 4 0.0 +overlapping count 15, 17 0.0 +overlapping count 9, 18 2.0 +overlapping count 3, 8 2.0 +overlapping count 11, 12 0.0 +overlapping count 9, 10 1.0 +overlapping count 8, 9 0.0 +overlapping count 8, 8 0.0 +overlapping count 5, 6 0.0 +overlapping count 3, 3 0.0 +overlapping count 3, 12 5.0 +overlapping count -1, 2 0.0 +overlapping count 0, 45 6.0 +overlapping count 13, 15 0.0 +-1 0.0 +0 0.0 +1 0.0 +2 0.0 +3 2.0 +4 2.0 +5 3.0 +6 3.0 +7 3.0 +8 3.0 +9 3.0 +10 3.0 +11 2.0 +12 2.0 +13 0.0 +14 0.0 +15 1.0 +16 1.0 +17 1.0 +18 1.0 +19 0.0 +20 0.0 +21 0.0 +22 0.0 +23 0.0 +24 0.0 +25 0.0 +26 0.0 +27 0.0 +28 0.0 +29 0.0 +30 0.0 +overlapping count 3, 4 2.0 +overlapping count 2, 3 2.0 +overlapping count 3, 8 4.0 +overlapping count 11, 12 2.0 +overlapping count 9, 10 3.0 +overlapping count 8, 9 4.0 +overlapping count 8, 8 3.0 +overlapping count 5, 6 3.0 +overlapping count 3, 3 2.0 +overlapping count 3, 12 5.0 +overlapping count -1, 2 0.0 +overlapping count 0, 45 6.0 +overlapping count 13, 15 1.0 +[main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 +[ {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 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 1 +decoding: 2 +decoding: 3 +decoding: 4 +decoding: 3 +decoding: 1 +decoding: 2 +decoding: 1 +decoding: 2 +decoding: 3 +decoding: 1 +decoding: 2 +decoding: 1 +decoding: 2 +decoding: 1 +[ {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {0} {1} {0} {0} {1} {1} {1} {0} {0} {0} {1} {0} {1} {0} {0} {1} {0} {0} {0} {1} {1} {0} {1} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {1} {1} {0} {1} {0} {0} {1} {0} {0} {1} |Encoded in 72 bits +[ {00110011001100100011001001110001010010001101010110100101101001} {0} {0}decoding: 0 + {1} {0}decoding: 4 + {0} {0}decoding: 4 + {0} {0}decoding: 4 + {0}decoding: 4 + {0}decoding: 4 + {0}decoding: 4 +decoding: 4 + {0}decoding: 4 + {0}decoding: 4 +decoding: 4 + {0}decoding: 4 +decoding: 4 + {0}decoding: 4 +decoding: 4 + {0} {0} {0} {0} {0}decoding: 1 + {0} {0} {0} {0}decoding: 2 + {0} {0} {0} {0} {0}decoding: 3 +decoding: 4 + {0} {0} {0} {0}decoding: 3 + {0} {0} {0}decoding: 1 + {0} {0} {0} {0}decoding: 2 + {0} {0} {0}decoding: 1 + {0} {0} {0}decoding: 2 + {0} {0} {0} {0}decoding: 3 + {0} {0} {0}decoding: 1 + {0} {0} {0}decoding: 2 + {0} {0}decoding: 1 + {0} {0} {0}decoding: 2 + {0} {0}decoding: 1 +[ {N:2} {0010} {N:5} {011111} {N:5} {/0/00///01} {N:3} {//0/0/} {N:15} {///////////00//0010} |Encoded in 80 bits +[ {N:2} {00101111010111111111011010011101111011110101110001111111111111} {1} {1} {1} {0} {0} {1} {1} | ->10 {N:5} {01111111110110100111011110111101011100011111111111111110011001} {0} {1} {1} {0} {0} {0} {0} {0} {0} | ->22 {N:5} {10100111011110111101011100011111111111111110011001011000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->38 {N:3} {11010111000111111111111111100110010110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->50 {N:15} {11111111111001100101100000000000000000000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->79decoding: 0 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 4 +decoding: 1 +decoding: 2 +decoding: 3 +decoding: 4 +decoding: 3 +decoding: 1 +decoding: 2 +decoding: 1 +decoding: 2 +decoding: 3 +decoding: 1 +decoding: 2 +decoding: 1 +decoding: 2 +decoding: 1 +10:09:04.212 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 +10:09:04.212 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds +10:09:04.360 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +10:09:04.403 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +10:09:04.403 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +10:09:04.421 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +10:09:04.421 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +10:09:04.563 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +10:09:04.610 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. +10:09:04.610 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +10:09:04.770 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +10:09:04.808 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] ] +[ 2 [2.576842E-5, 4.294736666666667E-4] ] +[ 3 [9.814783E-5, 9.471342857142858E-4] ] +[ 4 [1.05261E-4, 9.471342857142858E-4] ] +[ 5 [1.241481E-4, 9.471342857142858E-4] ] +[ 6 [1.325988E-4, 9.471342857142858E-4] ] +[ 7 [1.568503E-4, 9.803143750000002E-4] ] +[ 8 [2.254557E-4, 0.0012525316666666666] ] +[ 9 [3.79538E-4, 0.00189769] ] +[ 10 [6.114943E-4, 0.0027795195454545455] ] +[ 11 [0.001613954, 0.006724808333333334] ] +[ 12 [0.00330243, 0.012636935714285714] ] +[ 13 [0.003538342, 0.012636935714285714] ] +[ 14 [0.005236997, 0.017456656666666667] ] +[ 15 [0.006831909, 0.020762429411764708] ] +[ 16 [0.007059226, 0.020762429411764708] ] +[ 17 [0.008805129, 0.024458691666666667] ] +[ 18 [0.00940104, 0.02473957894736842] ] +[ 19 [0.01129798, 0.028244949999999998] ] +[ 20 [0.02115017, 0.050357547619047614] ] +[ 21 [0.04922736, 0.11188036363636364] ] +[ 22 [0.06053298, 0.1304633125] ] +[ 23 [0.06262239, 0.1304633125] ] +[ 24 [0.07395153, 0.14790306] ] +[ 25 [0.08281103, 0.15925198076923075] ] +[ 26 [0.08633331, 0.1598765] ] +[ 27 [0.1190654, 0.21261678571428572] ] +[ 28 [0.1890796, 0.32599931034482754] ] +[ 29 [0.2058494, 0.3430823333333333] ] +[ 30 [0.2209214, 0.3563248387096774] ] +[ 31 [0.2856, 0.44625000000000004] ] +[ 32 [0.3048895, 0.4619537878787878] ] +[ 33 [0.4660682, 0.6835770833333333] ] +[ 34 [0.4830809, 0.6835770833333333] ] +[ 35 [0.4921755, 0.6835770833333333] ] +[ 36 [0.5319453, 0.718845] ] +[ 37 [0.575155, 0.7414352564102564] ] +[ 38 [0.5783195, 0.7414352564102564] ] +[ 39 [0.6185894, 0.7626062790697675] ] +[ 40 [0.636362, 0.7626062790697675] ] +[ 41 [0.6448587, 0.7626062790697675] ] +[ 42 [0.6558414, 0.7626062790697675] ] +[ 43 [0.6885884, 0.7824868181818182] ] +[ 44 [0.7189864, 0.7988737777777778] ] +[ 45 [0.8179539, 0.8802645744680851] ] +[ 46 [0.8274487, 0.8802645744680851] ] +[ 47 [0.89713, 0.9304775510204082] ] +[ 48 [0.911868, 0.9304775510204082] ] +[ 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 [0.9944061322177664, 0.5007843707915816, -0.008092901782480327, -0.9977385576434543, 0.0, 0.0] ] + +truncated fdr=3.53108e-05 original=3.53108e-05 +truncated fdr=0.00128842 original=0.00128842 +truncated fdr=0.00128842 original=0.00128842 +truncated fdr=0.00284140 original=0.00284140 +truncated fdr=0.00284140 original=0.00284140 +truncated fdr=0.00284140 original=0.00284140 +truncated fdr=0.00284140 original=0.00284140 +truncated fdr=0.00294094 original=0.00294094 +truncated fdr=0.00375760 original=0.00375760 +truncated fdr=0.00569307 original=0.00569307 +truncated fdr=0.00833856 original=0.00833856 +truncated fdr=0.0201744 original=0.0201744 +truncated fdr=0.0379108 original=0.0379108 +truncated fdr=0.0379108 original=0.0379108 +truncated fdr=0.0523700 original=0.0523700 +truncated fdr=0.0622873 original=0.0622873 +truncated fdr=0.0622873 original=0.0622873 +truncated fdr=0.0733761 original=0.0733761 +truncated fdr=0.0742187 original=0.0742187 +truncated fdr=0.0847349 original=0.0847349 +truncated fdr=0.151073 original=0.151073 +truncated fdr=0.335641 original=0.335641 +truncated fdr=0.391390 original=0.391390 +truncated fdr=0.391390 original=0.391390 +truncated fdr=0.443709 original=0.443709 +truncated fdr=0.477756 original=0.477756 +truncated fdr=0.479630 original=0.479630 +truncated fdr=0.637850 original=0.637850 +truncated fdr=0.977998 original=0.977998 +truncated fdr=1.00000 original=1.00000 +truncated fdr=1.00000 original=1.00000 +truncated fdr=1.00000 original=1.00000 +truncated fdr=1.00000 original=1.00000 +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 42 threads. +Creating base test directory: test-results/stats-writer +allele: A ref: [CC] alt: [T]##fileformat=VCFv4.1 +##Goby=UNKNOWN +##FieldGroupAssociations=CHROM=genomic-coordinate,CHROM=cross-sample-field,POS=genomic-coordinate,POS=cross-sample-field,ID=external-identifiers,ID=cross-sample-field,REF=cross-sample-field,ALT=cross-sample-field,QUAL=cross-sample-field,FILTER=cross-sample-field,INFO=cross-sample-field,INFO/p-value1=cross-sample-field,INFO/p-value1=p-value,INFO/p-value2=cross-sample-field,INFO/p-value2=p-value,INFO/#Cm_Group[Group_1]=cross-sample-field,INFO/#Cm_Group[Group_1]=#Cm,FORMAT/Zygosity=zygozity,FORMAT/Zygosity=sample-data,FORMAT/Another=another,FORMAT/Another=sample-data, +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SampleA SampleB + +10:09:15.913 INFO BullardUpperQuartileNormalization - normalization denominator 46104.9 for sample B-7 +10:09:15.913 INFO BullardUpperQuartileNormalization - normalization denominator 45611.8 for sample B-3 +10:09:15.913 INFO BullardUpperQuartileNormalization - normalization denominator 93565.8 for sample A-3 +10:09:15.913 INFO BullardUpperQuartileNormalization - normalization denominator 93072.7 for sample A-12 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 46967.8 for sample B-15 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 46166.5 for sample B-14 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 44810.5 for sample B-11 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 93627.4 for sample A-17 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 45550.1 for sample B-2 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 46413.1 for sample B-10 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 90545.5 for sample A-16 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 47214.3 for sample B-8 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 44810.5 for sample B-4 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 92024.8 for sample A-2 +10:09:15.914 INFO BullardUpperQuartileNormalization - normalization denominator 90607.2 for sample A-0 +10:09:15.915 INFO BullardUpperQuartileNormalization - normalization denominator 45735.0 for sample B-6 +10:09:15.915 INFO BullardUpperQuartileNormalization - normalization denominator 89990.8 for sample A-9 +10:09:15.915 INFO BullardUpperQuartileNormalization - normalization denominator 93565.8 for sample A-8 +10:09:15.915 INFO BullardUpperQuartileNormalization - normalization denominator 93134.3 for sample A-5 +10:09:15.915 INFO BullardUpperQuartileNormalization - normalization denominator 92887.8 for sample A-4 +10:09:15.915 INFO BullardUpperQuartileNormalization - normalization denominator 91531.7 for sample A-6 +10:09:15.915 INFO BullardUpperQuartileNormalization - normalization denominator 93134.3 for sample A-7 +10:09:15.915 INFO BullardUpperQuartileNormalization - normalization denominator 47584.2 for sample B-5 +10:09:15.915 INFO BullardUpperQuartileNormalization - normalization denominator 94243.8 for sample A-10 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 94490.3 for sample A-14 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 45858.3 for sample B-9 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 93689.0 for sample A-1 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 45920.0 for sample B-0 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 46474.7 for sample B-12 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 46289.8 for sample B-13 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 93134.3 for sample A-19 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 95476.5 for sample A-18 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 93565.8 for sample A-15 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 46351.4 for sample B-1 +10:09:15.916 INFO BullardUpperQuartileNormalization - normalization denominator 94182.1 for sample A-13 +10:09:15.917 INFO BullardUpperQuartileNormalization - normalization denominator 95106.7 for sample A-11 +10:09:15.917 INFO BullardUpperQuartileNormalization - normalization denominator 45920.0 for sample B-16 +10:09:15.917 INFO BullardUpperQuartileNormalization - normalization denominator 46659.6 for sample B-17 +10:09:15.917 INFO BullardUpperQuartileNormalization - normalization denominator 46906.2 for sample B-19 +10:09:15.917 INFO BullardUpperQuartileNormalization - normalization denominator 45118.7 for sample B-18 +Creating base test directory: test-results/stats +[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. +[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. +[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. +[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. +[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. +[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. +[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. +[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. +Scanning target file.. +Target file had 1 entries. +Wrote 1 target ids to alignment header. +Setting quality threshold to 0.05 +Total logical entries written: 2 +Total bytes written: 0 +Average bytes/logical entry: 0.0 +Min query index: 0 +Max query index: 0 +Number of queries: 3 +Number of targets: 3 +Removed by quality filter: 0 +Not best score: 1 +Number of alignments written: 2 query_index: 0 target_index: 0 -position: 0 -query_position: 0 +position: 14977972 +score: 780.0 matching_reverse_strand: false -query_length: 75 -query_aligned_length: 75 -target_aligned_length: 75 -mapping_quality: 255 -pair_flags: 0 +multiplicity: 1 +number_of_mismatches: 1 +number_of_indels: 0 +query_length: 142 +query_aligned_length: 134 +target_aligned_length: 134 +sequence_variations { + to: "T" + from: "A" + position: 6 + to_quality: "/" + read_index: 14 +} fragment_index: 0 +query_index_occurrences: 2 ambiguity: 1 -query_index: 1 -target_index: 0 -position: 1 -query_position: 0 -matching_reverse_strand: false -query_length: 75 -query_aligned_length: 75 -target_aligned_length: 75 -mapping_quality: 255 -pair_flags: 0 -fragment_index: 0 -ambiguity: 1 +Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads +Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads +Converting [1/1] test-data/compact-reads/with-meta-data-input.compact-reads to will-not-write-here.compact-reads +Loading test-data/fdr-mode/file1.vcf +Loading test-data/fdr-mode/file2.vcf +Loading test-data/fdr-mode/file3.vcf +adjusting column: PCHI2 +Combining test-data/fdr-mode/file1.vcf +Combining test-data/fdr-mode/file2.vcf +Combining test-data/fdr-mode/file3.vcf +Loading test-data/fdr-mode/file-B-1.vcf +Loading test-data/fdr-mode/file-B-2.vcf +adjusting column: PCHI2 +Combining test-data/fdr-mode/file-B-1.vcf +Combining test-data/fdr-mode/file-B-2.vcf +Loading test-data/fdr-mode/file-B-1.vcf +Loading test-data/fdr-mode/file-B-2.vcf +adjusting column: PCHI2 +Combining test-data/fdr-mode/file-B-1.vcf +Combining test-data/fdr-mode/file-B-2.vcf +Loading test-data/fdr-mode/file1.vcf +Loading test-data/fdr-mode/file2.vcf +Loading test-data/fdr-mode/file3.vcf +Combining test-data/fdr-mode/file1.vcf +Combining test-data/fdr-mode/file2.vcf +Combining test-data/fdr-mode/file3.vcf +[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences + 1/1 ..T -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' -Processing queryIndex=19 with description '19 mismatch at end x2, starting at -1' -Processing queryIndex=20 with description '20 mismatch at end x5, starting at -1' -Processing queryIndex=21 with description '21 mismatch at end x1, starting at -2' -Processing queryIndex=22 with description '22 mismatch at end x2, starting at -2' -Processing queryIndex=23 with description '23 mismatch at end x5, starting at -2' -Processing queryIndex=12 with description '12 mismatch at beginning x1, starting at 1, with mutation at 20' -Processing queryIndex=13 with description '13 mismatch at beginning x2, starting at 1, with mutation at 20' -Processing queryIndex=15 with description '15 mismatch at beginning x1, starting at 2' -Processing queryIndex=16 with description '16 mismatch at beginning x2, starting at 2' -Processing queryIndex=14 with description '14 mismatch at beginning x5, starting at 1 (pos 4 actually does match), with mutation at 20' -Processing queryIndex=17 with description '17 mismatch at beginning x5, starting at 2 (pos 4 actually does match)' -Processing queryIndex=0 with description '0 perfect match' -Processing queryIndex=1 with description '1 perfect match on reverse strand' -Processing queryIndex=2 with description '2 mutation' -Processing queryIndex=3 with description '3 mutation on reverse strand' -Processing queryIndex=4 with description '4 insertion' -Processing queryIndex=6 with description '6 deletion' -Processing queryIndex=7 with description '7 deletion on reverse strand' -Processing queryIndex=27 with description '27 padding left & right, deletion then mutation' -Processing queryIndex=24 with description '24 padding left & right, mutation, deletion' -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' -01:32:43.845 WARN MessageChunksWriter - Using chunk-size=1000 -Total logical entries written: 20000 -Total bytes written: 77210 -Average bytes/logical entry: 3.8605 +Associating basename: basen0 to group: A +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:17.428 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 +10:09:17.429 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 +10:09:17.430 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 +10:09:17.432 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 +10:09:17.433 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 +10:09:17.435 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 +10:09:17.436 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 +10:09:17.438 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 +10:09:17.439 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 +10:09:17.440 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:17.513 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. +[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 +10:09:17.515 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. +[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 +10:09:17.516 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 +10:09:17.517 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 +10:09:17.519 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 +10:09:17.520 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 +10:09:17.521 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 +10:09:17.523 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 +10:09:17.524 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 +10:09:17.526 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:17.586 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 +10:09:17.587 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 +10:09:17.589 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 +10:09:17.590 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 +10:09:17.591 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 +10:09:17.593 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 +10:09:17.594 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 +10:09:17.595 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 +10:09:17.596 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 +10:09:17.598 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:17.684 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 +10:09:17.686 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 +10:09:17.687 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 +10:09:17.689 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 +10:09:17.690 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 +10:09:17.691 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 +10:09:17.693 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 +10:09:17.694 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 +10:09:17.695 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 +10:09:17.696 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:17.751 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 +10:09:17.753 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 +10:09:17.754 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 +10:09:17.755 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 +10:09:17.756 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 +10:09:17.757 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 +10:09:17.759 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 +10:09:17.760 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 +10:09:17.761 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 +10:09:17.762 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:17.824 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 +10:09:17.825 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 +10:09:17.826 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 +10:09:17.827 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 +10:09:17.828 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 +10:09:17.830 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 +10:09:17.831 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 +10:09:17.832 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 +10:09:17.833 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 +10:09:17.835 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:17.895 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 +10:09:17.896 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 +10:09:17.897 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 +10:09:17.898 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 +10:09:17.899 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 +10:09:17.901 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 +10:09:17.902 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 +10:09:17.903 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 +10:09:17.904 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 +10:09:17.906 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:17.956 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 +10:09:17.957 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 +10:09:17.958 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 +10:09:17.960 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 +10:09:17.961 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 +10:09:17.962 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 +10:09:17.963 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 +10:09:17.964 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 +10:09:17.965 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 +10:09:17.967 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:18.023 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 +10:09:18.024 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 +10:09:18.025 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 +10:09:18.026 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 +10:09:18.027 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 +10:09:18.028 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 +10:09:18.029 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 +10:09:18.030 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 +10:09:18.032 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 +10:09:18.033 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:18.127 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 +10:09:18.128 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 +10:09:18.129 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 +10:09:18.131 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 +10:09:18.132 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 +10:09:18.133 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 +10:09:18.134 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 +10:09:18.135 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 +10:09:18.136 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 +10:09:18.136 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +Comparing A/B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Filtering reads that have these criteria: +q<30 +#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 +10:09:18.188 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 +10:09:18.189 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 +10:09:18.191 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 +10:09:18.192 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 +10:09:18.193 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 +10:09:18.193 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 +10:09:18.194 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 +10:09:18.195 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 +10:09:18.196 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 +10:09:18.197 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 +Associating basename: basen1 to group: A +Associating basename: basen2 to group: A +Associating basename: basen3 to group: A +Associating basename: basen4 to group: A +Associating basename: basen5 to group: B +Associating basename: basen6 to group: B +Associating basename: basen7 to group: B +Associating basename: basen8 to group: B +Associating basename: basen9 to group: B +sample: basen0 group A +sample: basen2 group A +sample: basen4 group A +sample: basen3 group A +sample: basen1 group A +sample: basen9 group B +sample: basen6 group B +sample: basen5 group B +sample: basen7 group B +sample: basen8 group B +Using processor NONE +Methylation format ignores thresholdDistinctReadIndices. Additionally, the minimum coverage needed for a site to be reported can be changed with --minimum-variation-support. +Filtering reads that have these criteria: +[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 +10:09:18.255 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 +10:09:18.257 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 +10:09:18.258 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 +10:09:18.259 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 +10:09:18.260 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 +10:09:18.261 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 +10:09:18.262 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 +10:09:18.263 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 +10:09:18.264 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 +10:09:18.266 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 +info: + ref: A s=0 +info: + ref: A s=0 +info: + ref: A s=0 +info: + ref: A s=0 +info: + /T q=40 s=0 +info: - /T q=40 s=0 +info: + /C q=10 s=0 +info: + /C q=20 s=0 +info: + /C q=30 s=0 +info: + /C q=40 s=0 +info: + /C q=40 s=0 +info: + /C q=40 s=0 +info: + /C q=40 s=0 +info: + /C q=10 s=0 +info: + /C q=20 s=0 +info: + /N q=30 s=0 +info: + ref: A s=1 +info: + ref: A s=1 +info: + ref: A s=1 +info: + ref: A s=1 +info: + ref: A s=1 +info: + ref: A s=1 +info: + ref: A s=1 +info: + ref: A s=1 +info: + ref: A s=1 +info: + ref: A s=1 +info: + /T q=40 s=1 +info: + /T q=10 s=1 +info: + /T q=20 s=1 +info: + /T q=30 s=1 +info: + /N q=40 s=1 +info: + /N q=40 s=1 +list: pos=-1 #bases: 33 #indels: 0 +filtered: {+ ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + ref: A s=0, + /C q=10 s=0, + /C q=20 s=0, + /C q=30 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=40 s=0, + /C q=10 s=0, + /C q=20 s=0, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + ref: A s=1, + /T q=40 s=1, + /T q=10 s=1, + /T q=20 s=1, + /T q=30 s=1, + /N q=40 s=1, + /N q=40 s=1} +TTC[27]->CGT[27] / qual=1:2:3 +A[15]->G[20] / qual=20 +A[15]->G[20] / qual=20 +Processing test-data/sample-qual-scores/30reads.fa +Processed 0 read entries. +Min quality score: 2147483647 +Max quality score: -2147483648 +Avg quality score: 0 +Probable quality encoding scheme: fasta +Processing test-data/sample-qual-scores/30reads.fq +Processed 30 read entries. +Min quality score: 69 +Max quality score: 98 +Avg quality score: 94 +Probable quality encoding scheme: Illumina/Solexa +field CHROM value: 0 +field POS value: 145497099 +field ID value: . +field REF value: A +field ALT value: G +field QUAL value: 17.1 +field FILTER value: . +field INFO[DP] value: 2 +field INFO[DP4] value: 0,0,2,0 +field INFO[MQ] value: 25 +field INFO[FQ] value: -30.8 +field INFO[AF1] value: 0.9999 +field INFO[CI95] value: 0.5,1 +field INFO[PV4] value: +field INFO[INDEL] value: INDEL +field INFO[PC2] value: 3,3 +field INFO[PCHI2] value: 0.752 +field INFO[QCHI2] value: 1 +field INFO[RP] value: +field FORMAT[GT] value: +field FORMAT[GQ] value: +field FORMAT[GL] value: +field FORMAT[DP] value: +field FORMAT[SP] value: +field FORMAT[PL] value: +field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1 +field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42 +field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: +field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: +field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: +field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0 +field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1 +field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42 +field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: +field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: +field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: +field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0 +field CHROM gfi:0 value: 0 +field POS gfi:1 value: 145497099 +field ID gfi:2 value: . +field REF gfi:3 value: A +field ALT gfi:4 value: G +field QUAL gfi:5 value: 17.1 +field FILTER gfi:6 value: . +field FORMAT[GT] gfi:7 value: +field FORMAT[GQ] gfi:8 value: +field FORMAT[GL] gfi:9 value: +field FORMAT[DP] gfi:10 value: +field FORMAT[SP] gfi:11 value: +field FORMAT[PL] gfi:12 value: +field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1 +field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11 +field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: +field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: +field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: +field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0 +field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1 +field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42 +field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: +field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: +field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: +field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0 +Total logical entries written: 1 +Total bytes written: 0 +Average bytes/logical entry: 0.0 Min query index: 0 -Max query index: 1999 -Number of queries: 2000 -Number of targets: 10 -01:32:43.972 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 -01:32:43.972 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds +Max query index: 0 +Number of queries: 1 +Number of targets: 45 original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT -[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 72.892 s - in TestSuite + appending (count=0,length=1) + appending (count=4,length=3) + appending (count=1,length=3) + appending (count=0,length=2) + appending (count=3,length=1) + appending (count=1,length=1) + appending (count=0,length=1) + appending (count=4,length=3) + appending (count=0,length=5) + appending (count=3,length=1) + appending (count=0,length=2) + appending (count=2,length=1) + appending (count=0,length=2) + appending (count=3,length=1) + appending (count=2,length=1) + appending (count=0,length=1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=6 count=1 +(0,1) +loading transition for reader[0] position=1 length=3 count=3 +(0,1)(1,4) +loading transition for reader[0] position=4 length=2 count=0 +(0,1)(1,4)(4,1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=4 count=0 +(0,0) +loading transition for reader[0] position=1 length=1 count=1 +(0,0)(1,1) +loading transition for reader[0] position=2 length=4 count=0 +(0,0)(1,1)(2,0) +loading transition for reader[1] position=4 length=10 count=1 +(0,0)(1,1)(2,0)(4,1) +loading transition for reader[0] position=6 length=2 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2) +loading transition for reader[0] position=8 length=1 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1) +loading transition for reader[0] position=9 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) +loading transition for reader[0] position=10 length=2 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) +loading transition for reader[0] position=12 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) +loading transition for reader[0] position=13 length=3 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) +loading transition for reader[0] position=16 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=4 count=0 +loading transition for reader[0] position=1 length=1 count=1 +loading transition for reader[0] position=2 length=4 count=0 +loading transition for reader[1] position=4 length=10 count=1 +loading transition for reader[0] position=6 length=2 count=1 +loading transition for reader[0] position=8 length=1 count=0 +loading transition for reader[0] position=9 length=1 count=1 +loading transition for reader[0] position=10 length=2 count=0 +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 +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=6 count=1 +(0,1) +loading transition for reader[0] position=1 length=3 count=3 +(0,1)(1,4) +loading transition for reader[0] position=4 length=2 count=0 +(0,1)(1,4)(4,1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=4 count=0 +(0,0) +loading transition for reader[0] position=1 length=1 count=1 +(0,0)(1,1) +loading transition for reader[0] position=2 length=4 count=0 +(0,0)(1,1)(2,0) +loading transition for reader[1] position=4 length=10 count=1 +(0,0)(1,1)(2,0)(4,1) +loading transition for reader[0] position=6 length=2 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2) +loading transition for reader[0] position=8 length=1 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1) +loading transition for reader[0] position=9 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2) +loading transition for reader[0] position=10 length=2 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1) +loading transition for reader[0] position=12 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2) +loading transition for reader[0] position=13 length=3 count=0 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1) +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0) +loading transition for reader[0] position=16 length=1 count=1 +(0,0)(1,1)(2,0)(4,1)(6,2)(8,1)(9,2)(10,1)(12,2)(13,1)(14,0)(16,1) +loading transition for reader[0] position=0 length=1 count=0 +loading transition for reader[1] position=0 length=4 count=0 +loading transition for reader[0] position=1 length=1 count=1 +loading transition for reader[0] position=2 length=4 count=0 +loading transition for reader[1] position=4 length=10 count=1 +loading transition for reader[0] position=6 length=2 count=1 +loading transition for reader[0] position=8 length=1 count=0 +loading transition for reader[0] position=9 length=1 count=1 +loading transition for reader[0] position=10 length=2 count=0 +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 +loading transition for reader[0] position=0 length=1 count=0 +(0,0) +loading transition for reader[0] position=1 length=3 count=1 +(0,0)(1,1) +Appending count: 48124 length: 8 +Appending count: 24635 length: 9 +Appending count: 26777 length: 7 +Appending count: 30967 length: 4 +Appending count: 18154 length: 7 +Appending count: 2877 length: 8 +Appending count: 38231 length: 3 +Appending count: 9683 length: 8 +Appending count: 614 length: 9 +Appending count: 23931 length: 4 +Appending count: 41056 length: 9 +Appending count: 45634 length: 4 +Appending count: 42846 length: 7 +Appending count: 40630 length: 7 +Appending count: 8269 length: 1 +Appending count: 14229 length: 4 +Appending count: 43696 length: 1 +Appending count: 16832 length: 3 +Appending count: 29509 length: 9 +Appending count: 49230 length: 10 +Appending count: 28256 length: 1 +Appending count: 4221 length: 7 +Appending count: 11811 length: 1 +Appending count: 20419 length: 4 +Appending count: 29055 length: 8 +Appending count: 1427 length: 9 +Appending count: 31140 length: 10 +Appending count: 31019 length: 3 +Appending count: 33892 length: 8 +Appending count: 35337 length: 2 + position= 0 count= 48124 + position= 1 count= 48124 + position= 2 count= 48124 + position= 3 count= 48124 + position= 4 count= 48124 + position= 5 count= 48124 + position= 6 count= 48124 + position= 7 count= 48124 + position= 8 count= 24635 + position= 9 count= 24635 + position= 10 count= 24635 + position= 11 count= 24635 + position= 12 count= 24635 + position= 13 count= 24635 + position= 14 count= 24635 + position= 15 count= 24635 + position= 16 count= 24635 + position= 17 count= 26777 + position= 18 count= 26777 + position= 19 count= 26777 + position= 20 count= 26777 + position= 21 count= 26777 + position= 22 count= 26777 + position= 23 count= 26777 + position= 24 count= 30967 + position= 25 count= 30967 + position= 26 count= 30967 + position= 27 count= 30967 + position= 28 count= 18154 + position= 29 count= 18154 + position= 30 count= 18154 + position= 31 count= 18154 + position= 32 count= 18154 + position= 33 count= 18154 + position= 34 count= 18154 + position= 35 count= 2877 + position= 36 count= 2877 + position= 37 count= 2877 + position= 38 count= 2877 + position= 39 count= 2877 + position= 40 count= 2877 + position= 41 count= 2877 + position= 42 count= 2877 + position= 43 count= 38231 + position= 44 count= 38231 + position= 45 count= 38231 + position= 46 count= 9683 + position= 47 count= 9683 + position= 48 count= 9683 + position= 49 count= 9683 + position= 50 count= 9683 + position= 51 count= 9683 + position= 52 count= 9683 + position= 53 count= 9683 + position= 54 count= 614 + position= 55 count= 614 + position= 56 count= 614 + position= 57 count= 614 + position= 58 count= 614 + position= 59 count= 614 + position= 60 count= 614 + position= 61 count= 614 + position= 62 count= 614 + position= 63 count= 23931 + position= 64 count= 23931 + position= 65 count= 23931 + position= 66 count= 23931 + position= 67 count= 41056 + position= 68 count= 41056 + position= 69 count= 41056 + position= 70 count= 41056 + position= 71 count= 41056 + position= 72 count= 41056 + position= 73 count= 41056 + position= 74 count= 41056 + position= 75 count= 41056 + position= 76 count= 45634 + position= 77 count= 45634 + position= 78 count= 45634 + position= 79 count= 45634 + position= 80 count= 42846 + position= 81 count= 42846 + position= 82 count= 42846 + position= 83 count= 42846 + position= 84 count= 42846 + position= 85 count= 42846 + position= 86 count= 42846 + position= 87 count= 40630 + position= 88 count= 40630 + position= 89 count= 40630 + position= 90 count= 40630 + position= 91 count= 40630 + position= 92 count= 40630 + position= 93 count= 40630 + position= 94 count= 8269 + position= 95 count= 14229 + position= 96 count= 14229 + position= 97 count= 14229 + position= 98 count= 14229 + position= 99 count= 43696 + position= 100 count= 16832 + position= 101 count= 16832 + position= 102 count= 16832 + position= 103 count= 29509 + position= 104 count= 29509 + position= 105 count= 29509 + position= 106 count= 29509 + position= 107 count= 29509 + position= 108 count= 29509 + position= 109 count= 29509 + position= 110 count= 29509 + position= 111 count= 29509 + position= 112 count= 49230 + position= 113 count= 49230 + position= 114 count= 49230 + position= 115 count= 49230 + position= 116 count= 49230 + position= 117 count= 49230 + position= 118 count= 49230 + position= 119 count= 49230 + position= 120 count= 49230 + position= 121 count= 49230 + position= 122 count= 28256 + position= 123 count= 4221 + position= 124 count= 4221 + position= 125 count= 4221 + position= 126 count= 4221 + position= 127 count= 4221 + position= 128 count= 4221 + position= 129 count= 4221 + position= 130 count= 11811 + position= 131 count= 20419 + position= 132 count= 20419 + position= 133 count= 20419 + position= 134 count= 20419 + position= 135 count= 29055 + position= 136 count= 29055 + position= 137 count= 29055 + position= 138 count= 29055 + position= 139 count= 29055 + position= 140 count= 29055 + position= 141 count= 29055 + position= 142 count= 29055 + position= 143 count= 1427 + position= 144 count= 1427 + position= 145 count= 1427 + position= 146 count= 1427 + position= 147 count= 1427 + position= 148 count= 1427 + position= 149 count= 1427 + position= 150 count= 1427 + position= 151 count= 1427 + position= 152 count= 31140 + position= 153 count= 31140 + position= 154 count= 31140 + position= 155 count= 31140 + position= 156 count= 31140 + position= 157 count= 31140 + position= 158 count= 31140 + position= 159 count= 31140 + position= 160 count= 31140 + position= 161 count= 31140 + position= 162 count= 31019 + position= 163 count= 31019 + position= 164 count= 31019 + position= 165 count= 33892 + position= 166 count= 33892 + position= 167 count= 33892 + position= 168 count= 33892 + position= 169 count= 33892 + position= 170 count= 33892 + position= 171 count= 33892 + position= 172 count= 33892 + position= 173 count= 35337 + position= 174 count= 35337 + peak : start :5 count :13 length :100010 + peak : start :100020 count :10 length :1 +10:09:18.816 WARN WiggleWindow - Not writing 101 7 +10:09:18.816 WARN WiggleWindow - Not writing 111 7 +10:09:18.816 WARN WiggleWindow - Not writing 131 8 +10:09:18.816 WARN WiggleWindow - Not writing 141 8 +10:09:18.816 WARN WiggleWindow - Not writing 151 8 + appending (count=10,length=4) + appending (count=1,length=0) + appending (count=2,length=8) +Hello + appending (count=10,length=4) + 0 +AAC 3 +ACC 6 +ATC 9 +AGC 12 +AAC 15 +ACC 18 +ATC 21 +AGC 24 +AAC 27 +ACC 30 +ATC 33 +AGC 36 +AAC 39 +ACC 42 +ATC 45 +AGC 48 +AAC 51 +ACC 54 +ATC 57 +AGC 60 +AAC 63 +ACC 66 +ATC 69 +AGC 72 +AAC 75 +ACC 78 +ATC 81 +AGC10:09:18.881 WARN MessageChunksWriter - Using chunk-size=9 +10:09:18.883 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 +10:09:18.885 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 +10:09:18.887 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 +qPhred=1 +qPhred=2 +qPhred=3 +qPhred=4 +qPhred=5 +qPhred=6 +qPhred=7 +qPhred=8 +qPhred=9 +qPhred=10 +qPhred=11 +qPhred=12 +qPhred=13 +qPhred=14 +qPhred=15 +qPhred=16 +qPhred=17 +qPhred=18 +qPhred=19 +qPhred=20 +qPhred=21 +qPhred=22 +qPhred=23 +qPhred=24 +qPhred=25 +qPhred=26 +qPhred=27 +qPhred=28 +qPhred=29 +qPhred=30 +qPhred=31 +qPhred=32 +qPhred=33 +qPhred=34 +qPhred=35 +qPhred=36 +qPhred=37 +qPhred=38 +qPhred=39 +qPhred=40 +qPhred=41 +qPhred=42 +qPhred=43 +qPhred=44 +qPhred=45 +qPhred=46 +qPhred=47 +qPhred=48 +qPhred=49 +qPhred=50 +qPhred=51 +qPhred=52 +qPhred=53 +qPhred=54 +qPhred=55 +qPhred=56 +qPhred=57 +qPhred=58 +qPhred=59 +qPhred=60 +qPhred=61 +>1 +NNTGAATGAGACCTA + +[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 68.955 s - in TestSuite [INFO] [INFO] Results: [INFO] @@ -6684,14 +6709,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.051 s] -[INFO] Goby I/O ........................................... SUCCESS [ 7.004 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.050 s] +[INFO] Goby I/O ........................................... SUCCESS [ 13.802 s] [INFO] Goby Full Distribution ............................. SUCCESS [01:48 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:55 min -[INFO] Finished at: 2025-08-31T01:33:15-12:00 +[INFO] Total time: 02:02 min +[INFO] Finished at: 2026-10-04T10:09:54+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -6762,14 +6787,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.329 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.372 s] [INFO] Goby I/O ........................................... SUCCESS [ 0.048 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 0.047 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 0.036 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.619 s -[INFO] Finished at: 2025-08-31T01:33:17-12:00 +[INFO] Total time: 0.605 s +[INFO] Finished at: 2026-10-04T10:09:56+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... @@ -6780,12 +6805,12 @@ > 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 -Aug 31, 2025 1:33:23 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Oct 04, 2026 10:10:02 AM org.debian.maven.packager.DependenciesSolver$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 -Aug 31, 2025 1:33:28 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +Oct 04, 2026 10:10:07 AM org.debian.maven.packager.DependenciesSolver$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 @@ -6812,11 +6837,11 @@ dh_missing 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: Depends field of package goby-java: substitution variable ${maven:Depends} used, but is not 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 -dpkg-gencontrol: warning: Depends field of package libgoby-io-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 dh_md5sums @@ -6830,12 +6855,14 @@ 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/1381621/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1381621/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/1358061 and its subdirectories -I: Current time: Sun Aug 31 01:33:45 -12 2025 -I: pbuilder-time-stamp: 1756647225 +I: removing directory /srv/workspace/pbuilder/1381621 and its subdirectories +I: Current time: Sun Oct 4 10:10:21 +14 2026 +I: pbuilder-time-stamp: 1791058221