Diff of the two buildlogs: -- --- b1/build.log 2024-05-07 07:17:47.478756090 +0000 +++ b2/build.log 2024-05-07 07:47:25.931053533 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Jun 9 01:36:02 -12 2025 -I: pbuilder-time-stamp: 1749476162 +I: Current time: Tue May 7 21:17:51 +14 2024 +I: pbuilder-time-stamp: 1715066271 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -43,52 +43,84 @@ dpkg-source: info: applying adding_opens_arg_for_tests.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/89880/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/4155971/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-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 May 7 07:18 /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/4155971/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/4155971/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=42 ' - DISTRIBUTION='trixie' - 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]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(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=20 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='ccc4e202b29548e48fda682e7b541549' - 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='89880' - PS1='# ' - PS2='> ' + INVOCATION_ID=11e03eb2170b49a48dd54500a2820b3b + 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=4155971 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.rFLny5uu/pbuilderrc_MChp --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rFLny5uu/b1 --logfile b1/build.log libgoby-java_3.3.1+dfsg2-10.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + 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.rFLny5uu/pbuilderrc_1ziB --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.rFLny5uu/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-10.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos15-amd64 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 8 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/89880/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 5 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/4155971/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -646,7 +678,7 @@ Get: 440 http://deb.debian.org/debian trixie/main amd64 r-base-core amd64 4.3.2-1 [26.8 MB] Get: 441 http://deb.debian.org/debian trixie/main amd64 r-cran-rjava amd64 1.0-11-1 [702 kB] Get: 442 http://deb.debian.org/debian trixie/main amd64 testng all 6.9.12-4 [795 kB] -Fetched 379 MB in 10s (38.9 MB/s) +Fetched 379 MB in 15s (25.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpipeline1: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 ... 19698 files and directories currently installed.) @@ -2078,8 +2110,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Jun 9 13:37:43 UTC 2025. -Universal Time is now: Mon Jun 9 13:37:43 UTC 2025. +Local time is now: Tue May 7 07:24:08 UTC 2024. +Universal Time is now: Tue May 7 07:24:08 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libgeronimo-annotation-1.3-spec-java (1.3-1) ... @@ -2647,7 +2679,11 @@ 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+dfsg2-10_source.changes +I: user script /srv/workspace/pbuilder/4155971/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/4155971/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+dfsg2-10_source.changes dpkg-buildpackage: info: source package libgoby-java dpkg-buildpackage: info: source version 3.3.1+dfsg2-10 dpkg-buildpackage: info: source distribution unstable @@ -2787,127 +2823,92 @@ [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings -[WARNING] Loading source files for package org.campagnelab.goby.R... -[WARNING] Loading source files for package org.campagnelab.goby.alignments... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... -[WARNING] Loading source files for package org.campagnelab.goby.baseinfo... -[WARNING] Loading source files for package org.campagnelab.goby... +[WARNING] Loading source files for package org.campagnelab.goby.methylation... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... +[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data... -[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges... -[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... +[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv... -[WARNING] Loading source files for package org.campagnelab.goby.util... -[WARNING] Loading source files for package org.campagnelab.goby.util.motifs... -[WARNING] Loading source files for package org.campagnelab.goby.util.barcode... -[WARNING] Loading source files for package org.campagnelab.goby.util.commits... -[WARNING] Loading source files for package org.campagnelab.goby.util.pool... -[WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... -[WARNING] Loading source files for package org.campagnelab.goby.stats... -[WARNING] Loading source files for package org.campagnelab.goby.modes... -[WARNING] Loading source files for package org.campagnelab.goby.modes.formats... -[WARNING] Loading source files for package org.campagnelab.goby.modes.core... -[WARNING] Loading source files for package org.campagnelab.goby.modes.dsv... +[WARNING] Loading source files for package org.campagnelab.goby.readers... [WARNING] Loading source files for package org.campagnelab.goby.readers.sam... [WARNING] Loading source files for package org.campagnelab.goby.readers.vcf... -[WARNING] Loading source files for package org.campagnelab.goby.readers... -[WARNING] Loading source files for package org.campagnelab.goby.xml... -[WARNING] Loading source files for package org.campagnelab.goby.predictions... [WARNING] Loading source files for package org.campagnelab.goby.counts... [WARNING] Loading source files for package org.campagnelab.goby.counts.compound... -[WARNING] Loading source files for package org.campagnelab.goby.exception... -[WARNING] Loading source files for package org.campagnelab.goby.cli... -[WARNING] Loading source files for package org.campagnelab.goby.compression... +[WARNING] Loading source files for package org.campagnelab.goby... [WARNING] Loading source files for package org.campagnelab.goby.parsers... [WARNING] Loading source files for package org.campagnelab.goby.reads... +[WARNING] Loading source files for package org.campagnelab.goby.R... +[WARNING] Loading source files for package org.campagnelab.goby.compression... [WARNING] Loading source files for package org.campagnelab.goby.config... -[WARNING] Loading source files for package org.campagnelab.goby.methylation... +[WARNING] Loading source files for package org.campagnelab.goby.modes... +[WARNING] Loading source files for package org.campagnelab.goby.modes.formats... +[WARNING] Loading source files for package org.campagnelab.goby.modes.core... +[WARNING] Loading source files for package org.campagnelab.goby.modes.dsv... +[WARNING] Loading source files for package org.campagnelab.goby.stats... +[WARNING] Loading source files for package org.campagnelab.goby.alignments... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... +[WARNING] Loading source files for package org.campagnelab.goby.exception... +[WARNING] Loading source files for package org.campagnelab.goby.util... +[WARNING] Loading source files for package org.campagnelab.goby.util.motifs... +[WARNING] Loading source files for package org.campagnelab.goby.util.pool... +[WARNING] Loading source files for package org.campagnelab.goby.util.commits... +[WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... +[WARNING] Loading source files for package org.campagnelab.goby.util.barcode... +[WARNING] Loading source files for package org.campagnelab.goby.baseinfo... +[WARNING] Loading source files for package org.campagnelab.goby.predictions... +[WARNING] Loading source files for package org.campagnelab.goby.cli... +[WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package samples... [WARNING] Loading source files for package org.campagnelab.dl.varanalysis.protobuf... [WARNING] Constructing Javadoc information... -[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] ^ -[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/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/methylation/MethylSimilarityScan.java:23: error: package org.apache.commons.cli does not exist +[WARNING] import org.apache.commons.cli.*; [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/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/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/GobyRengine.java:56: error: cannot find symbol -[WARNING] private 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] ^ -[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] /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/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:21: error: package javax.xml.bind.annotation does not exist +[WARNING] import javax.xml.bind.annotation.XmlAccessType; [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] /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] 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/AnnotationLength.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:50: error: cannot find symbol -[WARNING] public void rBusy(final Rengine rengine, final int which) { +[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 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: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:81: error: cannot find symbol -[WARNING] public void rShowMessage(final Rengine rengine, final String message) { +[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: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/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:101: error: cannot find symbol -[WARNING] public void rFlushConsole(final Rengine rengine) { +[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:111: error: cannot find symbol -[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) { +[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: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/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol +[WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ -[WARNING] symbol: class Rengine -[WARNING] location: class RConsoleMainLoopCallback +[WARNING] symbol: class XmlAccessorType [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] ^ @@ -2958,85 +2959,83 @@ [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/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/algorithmic/algorithm/dmr/FisherExactTestAdaptor.java:23: 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/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/data/xml/AnnotationLength.java:21: error: package javax.xml.bind.annotation does not exist -[WARNING] import javax.xml.bind.annotation.XmlAccessType; +[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/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/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/data/xml/AnnotationLength.java:29: error: cannot find symbol -[WARNING] @XmlAccessorType(XmlAccessType.FIELD) +[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] 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 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] ^ -[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] /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] 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] /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] 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] /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] 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] /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] 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 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] 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] 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] /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] 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] 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 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] ^ @@ -3078,6 +3077,29 @@ [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] ^ @@ -3099,6 +3121,9 @@ [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] ^ @@ -3108,25 +3133,35 @@ [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/CompareGroupsVCFOutputFormat.java:42: 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/modes/formats/BetweenGroupSequenceVariationOutputFormat.java:40: 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/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] 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/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/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/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/stats/FisherExactRCalculator.java:68: error: cannot find symbol +[WARNING] Rengine rEngine; [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] 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] ^ +[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/PlantIndels.java:22: 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/cli/DoInParallel.java:21: error: package edu.rit.pj does not exist [WARNING] import edu.rit.pj.ParallelTeam; [WARNING] ^ @@ -3140,15 +3175,16 @@ [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/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: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/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: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/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/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/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol [WARNING] @XmlAccessorType(XmlAccessType.FIELD) [WARNING] ^ @@ -3917,59 +3953,436 @@ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/serialized-form.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EquivalentIndelRegionCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/OneBinStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/StatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FastSmallAndLog10BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CumulativeArrayKeeperFast.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.TypeOfPair.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/LinearBinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log10BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/By5BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BuggyDeltaStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/RegionAveragingWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat3StatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PTestMciProviderStatisticAdaptor.html... +[WARNING] Generating 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Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Annotation.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Segment.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/CovariateInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/Interval.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/class-use/DistinctIntValueCounterBitSet.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Range.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/class-use/Ranges.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/AnnotationLength.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/InfoOutput.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/class-use/SampleTotalCount.html... +[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html... -[WARNING] 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html... +[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/HTSJdkReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingAlignmentWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SamRecordGenomicPositionComparator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingSamBamWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/BufferedSortingAlignmentWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentSliceHelper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadGroupHelper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ScanReferenceSequence.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionFacadeAlignmentReader.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/UpgradeTo1_9_6.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Merge.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadOriginInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentToTextWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionToBasesMap.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatSortedAlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentPositionComparator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SortIterateAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractConcatAlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/PositionBaseInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ExportableAlignmentEntryData.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/DefaultAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReferenceLocation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/EntryFlagHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractAlignmentReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractConcatAlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NoUpgradeAlignmentReaderFactory.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ConcatAlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/NonAmbiguousAlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderFactoryBase.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReadIndexStats.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Merge.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AbstractAlignmentReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentReaderImpl.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentTooManyHitsWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GenomicRange.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/GobyAlignmentReaderFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/ReferenceLocation.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/SamRecordGenomicPositionComparator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/LastParser.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentIndex.Builder.html... @@ -4004,522 +4417,129 @@ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/class-use/Alignments.AlignmentCollectionOrBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/class-use/BestScoreAmbiguityAlignmentFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutationReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReaderInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutation.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ConcatenatePermutations.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToSortedReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/ObservedIndel.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessorUnsorted.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToListIterator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DefaultAlignmentProcessorFactory.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/GenomeAlignmentTargetMapper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/RealignmentProcessor.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/LocalSortProcessor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DummyProcessorUnsorted.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/DefaultAlignmentProcessorFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReaderInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ConcatenatePermutations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutationReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/ReadNameToIndex.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/PermutationWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/NoOpPermutation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/class-use/QueryIndexPermutationInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorNumVariationsInRead.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/BasenameUtils.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorPairFlags.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToEndOfRead.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorReadMappingQuality.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorTargetAlignedLength.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistanceToStartOfRead.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/ConstantAccumulator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryPosition.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceSegmentInformationWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorDistancesToReadVariations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/CommitPropertiesStatAccumulator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryAlignedLength.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorInsertSizes.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorBaseQuality.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/class-use/Release1_9_7_2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/class-use/GobyVersion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html... 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html... -[WARNING] Generating 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitTranscriptsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FalseDiscoveryRateMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractGobyMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToAnnotationCountsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SplitFastaMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/WithinGroupVariabilityMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/MethylStatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateCompactReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/RunParallelMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/FilesToAttributesMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToTranscriptCountsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/InferSexFromAlignmentsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractCommandLineMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToBedGraphMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SomaticVariationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/CompareGroupsVCFOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/BetweenGroupSequenceVariationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRegionsOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/IndelCountOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CommonIndelArtifactFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.WillKeepI.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/PostBarcodeMatcher.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcherResult.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/class-use/BarcodeMatcher.html... +[WARNING] Generating 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+[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorPairFlags.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorQueryAlignedLength.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/SequenceBaseInformationWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/ConstantAccumulator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/class-use/StatAccumulatorBaseQuality.html... +[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/SomaticPredictor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/Predictor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html... 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html... -[WARNING] 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.Builder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePositionOrBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.Builder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.BaseOrBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.Builder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SampleOrBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.Builder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationOrBuilder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.Builder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/ParseReadsCodeSample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SomaticOutput.Builder.html... @@ -4539,6 +4559,22 @@ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollection.Builder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformationCollectionOrBuilder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePosition.Builder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.ReferencePositionOrBuilder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Base.Builder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.BaseOrBuilder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.Sample.Builder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SampleOrBuilder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformation.Builder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationOrBuilder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollection.Builder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/SegmentInformationRecords.SegmentInformationCollectionOrBuilder.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-use.html... @@ -4641,47 +4677,47 @@ [INFO] Adding the --ignore-source-errors option [INFO] No previous run data found, generating javadoc. [WARNING] Javadoc Warnings -[WARNING] Loading source files for package org.campagnelab.goby.R... -[WARNING] Loading source files for package org.campagnelab.goby.alignments... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... -[WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... -[WARNING] Loading source files for package org.campagnelab.goby.baseinfo... -[WARNING] Loading source files for package org.campagnelab.goby... +[WARNING] Loading source files for package org.campagnelab.goby.methylation... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels... +[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data... -[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... [WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.ranges... -[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression... +[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.data.xml... 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[WARNING] Loading source files for package org.campagnelab.goby.reads... +[WARNING] Loading source files for package org.campagnelab.goby.R... +[WARNING] Loading source files for package org.campagnelab.goby.compression... [WARNING] Loading source files for package org.campagnelab.goby.config... -[WARNING] Loading source files for package org.campagnelab.goby.methylation... +[WARNING] Loading source files for package org.campagnelab.goby.modes... +[WARNING] Loading source files for package org.campagnelab.goby.modes.formats... +[WARNING] Loading source files for package org.campagnelab.goby.modes.core... +[WARNING] Loading source files for package org.campagnelab.goby.modes.dsv... +[WARNING] Loading source files for package org.campagnelab.goby.stats... +[WARNING] Loading source files for package org.campagnelab.goby.alignments... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.perms... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.filters... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.processors... +[WARNING] Loading source files for package org.campagnelab.goby.alignments.htsjdk... +[WARNING] Loading source files for package org.campagnelab.goby.exception... +[WARNING] Loading source files for package org.campagnelab.goby.util... +[WARNING] Loading source files for package org.campagnelab.goby.util.motifs... +[WARNING] Loading source files for package org.campagnelab.goby.util.pool... +[WARNING] Loading source files for package org.campagnelab.goby.util.commits... +[WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions... +[WARNING] Loading source files for package org.campagnelab.goby.util.barcode... +[WARNING] Loading source files for package org.campagnelab.goby.baseinfo... +[WARNING] Loading source files for package org.campagnelab.goby.predictions... +[WARNING] Loading source files for package org.campagnelab.goby.cli... +[WARNING] Loading source files for package org.campagnelab.goby.xml... [WARNING] Loading source files for package samples... [WARNING] Constructing Javadoc information... [WARNING] Building index for all the packages and classes... @@ -5546,558 +5582,558 @@ [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/package-tree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/constant-values.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/serialized-form.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.Result.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/FisherExact.AlternativeHypothesis.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/class-use/GobyRengine.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentStats.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentWriterImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/RepositionableInputStream.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignedSequence.html... -[WARNING] Generating 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/class-use/HTSJDKReaderImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/SkipToListIterator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/GenomeAlignmentTargetMapper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorFactory.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/class-use/AlignmentProcessorInterface.html... -[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EquivalentIndelRegionCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/BaseProportionWeight.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SummedCombinator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/QFast.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FrequencyTable.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.ReadIndexInfo.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SequenceVariationPool.Variation.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATGCCorrectionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ExportSplicingEvents.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/GCProportionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FenwickTree.answer.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MedianCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountIterateAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/MaxCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HeptamerWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/LogGCCorrectionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCountInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/SortedAnnotations.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeCountInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationWeightCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/CoverageAnalysis.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeWeightCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/RandomAccessAnnotations.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightAnnotationCount.FormulaChoice.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ATProportionWeight.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/ComputeStartCount.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/HiCMerge.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/AnnotationCount.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/EvidenceCombinator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/FormulaWeightCount.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeltaStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/class-use/WeightCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DifferentiallyMethylatedRegion.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/OneBinStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FisherExactTestAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ChiSquareTestAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/DeNovoDMRfinder.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat4StatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SmallAndLog10BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/StatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/FastSmallAndLog10BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CumulativeArrayKeeperFast.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5MciProviderStatisticAdaptor.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/ObservationWriter.TypeOfPair.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/AbstractMethylationAdapter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/EstimatedDistribution.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/MethylationRateDifferenceStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SitesInFixedWindow.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PassThroughStatisticAdaptor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Log2BinningStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/CovariateStrategy.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/PVAlueProvider.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/SlidingCountArray.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/class-use/Stat5StatisticAdaptor.html... 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageFisherRCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeColumns.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProvider.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/RegionWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderFromRegionsOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ElementIndexComparator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/TSVWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/EstimatedTestDistributions.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeNonZeroNonNaN.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactTestCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AbstractOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionAnalysis.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BenjaminiHochbergAdjustment.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/RpkmLikeNormalizationMethod.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ChiSquareTestCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderTestSupport.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.html... -[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] ^ -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. -[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, -[WARNING] ^ -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BullardUpperQuartileNormalization.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleCountCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AlignedCountNormalization.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeMagnitudeCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DummyObservationWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/Log2FoldChangeCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/CountCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactRCalculator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/NormalizationMethod.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/VCFWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeCalculator.html... -[WARNING] 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ExtractSplicingEventsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/class-use/CountsReaderI.html... +[WARNING] 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+[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html... +[WARNING] 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToSAMMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiffAlignmentMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FalseDiscoveryRateMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TrimMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BarcodeDecoderMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToKnownIndelsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/UpgradeMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactFileStatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VersionMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BisulfiteConversionMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactSamHelperMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MergeCompactAlignmentsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToKnownIndelsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadQualityStatsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TestRConnectionMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BuildSequenceCacheMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToCountsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToReadSetMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CoverageMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/HeptamerWeightsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompareAlignmentToGenomeMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/Sort1Mode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SimulateReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractCommandLineMode.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DiscoverSequenceVariantsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByPeakDistanceMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadsToWeightsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/IterateSortedAlignmentsToPileup.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ConcatenateAlignmentMode.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplicedSamHelper.Limits.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReformatCompactReadsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/StatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ReadSetToTextMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactToFastaMode.OutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SplitCompactReadsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToWiggleMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SamExtractReadsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMComparisonMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SortMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/LastToCompactMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/EmpiricalPMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WithinGroupVariabilityMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/HeptamerWeightsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFToGenotypeMapMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToPileupMode.OutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/BaseStatsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SampleQualityScoresMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStats2Mode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/DisplaySequenceVariationsMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AlignmentToTextMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToUnionPeaksAnnotationMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TrimMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/FastaToCompactMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/PercentMismatchesQualityFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GobyDriver.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyBasesMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CompactAlignmentToReadSetMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AggregatePeaksByRPKMDifferenceMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TallyReadsMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFSubsetMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SuggestPositionSlicesMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TestRConnectionMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SequenceVariationStatsMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VCFCompareMode.VCFPosition.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/VcfToTabMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/WeightParameters.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AnnotationPenaltyMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/ColorSpaceConverter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/AbstractAlignmentToCompactMode.TransferIds.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/TabToColumnInfoMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/GenericToolsDriver.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/MethylationFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/SAMToCompactMode.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/class-use/CountsArchiveToBedGraphMode.html... 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/MethylationRateVCFOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceVariationOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/AlleleFrequencyOutputFormat.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/SequenceBaseInformationOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/class-use/GenotypesOutputFormat.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/TabToColumnInfoModeCore.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/class-use/UpgradeModeCore.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/QualityScoreFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/GenotypeFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveIndelArtifactsFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiploidFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CommonIndelArtifactFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/EntropicIndelArtifactFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/IterateSortedAlignmentsListImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/AtLeastAQuarterFilter.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerNoThresholdingEffect.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixerInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/RemoveBasesMatchingIndelsGenotypeFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/CountFixer.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/LeftOverFilter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SAMRecordIterable.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ChromosomeMapper.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConvertSamBAMReadToGobyAlignment.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/ConversionConfig.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparisonInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamPerPositionComparison.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamSegment.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobySamRecord.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamComparison.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/SamRecordParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/class-use/GobyQuickSeqvar.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnFields.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnMetaInfo.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/Columns.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnField.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/GroupAssociations.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/ColumnType.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/class-use/VCFParser.SyntaxException.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/class-use/FastXEntry.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/class-use/StrandBiasFilter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactRCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeDouble.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeColumns.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/InformativeNonZeroNonNaN.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SamplePair.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleCountCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BenjaminiHochbergAdjustment.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProvider.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MethylCountProviderFromRegionsOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionResults.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ElementIndexComparator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/TTestCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BonferroniAdjustment.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FisherExactTestCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/StatisticComparator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FormatFieldCounter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeMagnitudeCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/Log2FoldChangeCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/EstimatedTestDistributions.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageFisherRCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/VCFWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AlignedCountNormalization.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionAnalysis.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/TSVWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/EmpiricalPValueEstimator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DataProvider.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/RpkmLikeNormalizationMethod.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AbstractOutputFormat.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.html... +[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] ^ +[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.java:133: warning: @inheritDoc used but getDenominator(DifferentialExpressionCalculator, String) does not override or implement any method. +[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator, +[WARNING] ^ +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DifferentialExpressionCalculator.ElementType.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/CountCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/MinCombinator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/DummyObservationWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/SampleStats.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/BullardUpperQuartileNormalization.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/FoldChangeCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/ChiSquareTestCalculator.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AnnotationAveragingWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/class-use/AverageCalculator.html... +[WARNING] Generating 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+[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentCollectionHandler.CombinedLists.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/AlignmentToTextWriter.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/IterateSortedAlignments.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/class-use/FileSlice.html... +[WARNING] Generating 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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/MergeIndelFrom.SplitIndel.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF3.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/ProtoHelper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/DummyTrueGenotypeHelper.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/SomaticPredictor.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/FormatIndelVCF2.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/class-use/AddTrueGenotypeHelperI.html... 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/build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastBufferedMessageChunksReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/MessageChunksReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderOrder1.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoderI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/GZipChunkCodec.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderPlus.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderOrder1.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/GzipOutputStreamWithCustomLevel.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticDecoderI.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/FastArithmeticCoder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/class-use/InvalidChecksumException.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/FastaParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/class-use/ReaderFastaParser.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadSet.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodecImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsToTextWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadProtobuffCollectionHandler.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec2.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsReader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/PicardFastaIndexedSequence.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadCodec.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceEncoder.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriter.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/SequenceDigests.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceCache.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/QualityEncoding.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceTestSupport.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsWriterImpl.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/DualRandomAccessSequenceCache.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/RandomAccessSequenceInterface.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/ReadsLoader.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/MultiReads.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/class-use/CompressedRead.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/class-use/GobyConfiguration.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSite.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylSimilarityScan.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationData.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/DifferentiallyMethylatedRegion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationRegion.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/HitBoundedPriorityQueue.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSimilarityMatch.html... -[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:127: warning: Tag @link: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore -[WARNING] * Dequeues a document from the queue, returning an instance of {@link -[WARNING] ^ -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/class-use/MethylationSiteIterator.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseReadsCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/SimulateBisulfiteReads.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DumpTargetInfo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/DoInParallel.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/class-use/TestSkipTo.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/class-use/MethylStats.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesWithIndexCodeSample.html... -[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ModifyAlignmentsCodeSample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseAlignmentEntriesCodeSample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/ParseReadsCodeSample.html... +[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/class-use/IterateAlignmentsCodeSample.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-use.html... [WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-use.html... @@ -6194,14 +6230,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.034 s] -[INFO] Goby I/O ........................................... SUCCESS [ 17.067 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 19.087 s] +[INFO] Goby Framework ..................................... SUCCESS [ 0.175 s] +[INFO] Goby I/O ........................................... SUCCESS [02:34 min] +[INFO] Goby Full Distribution ............................. SUCCESS [02:07 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 36.277 s -[INFO] Finished at: 2025-06-09T01:38:49-12:00 +[INFO] Total time: 04:43 min +[INFO] Finished at: 2024-05-07T21:32:12+14:00 [INFO] ------------------------------------------------------------------------ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' @@ -6331,55 +6367,1732 @@ [INFO] T E S T S [INFO] ------------------------------------------------------- [INFO] Running TestSuite -01:39:01.712 INFO RLoggerMainLoopCallback - +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] +21:34:12.935 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 +21:34:13.282 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) +21:38:03.372 WARN WiggleWindow - Not writing 101 7 +21:38:03.372 WARN WiggleWindow - Not writing 111 7 +21:38:03.373 WARN WiggleWindow - Not writing 131 8 +21:38:03.373 WARN WiggleWindow - Not writing 141 8 +21:38:03.373 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: 38443 length: 3 +Appending count: 22996 length: 6 +Appending count: 22651 length: 10 +Appending count: 44478 length: 7 +Appending count: 31150 length: 9 +Appending count: 43500 length: 1 +Appending count: 30469 length: 4 +Appending count: 16769 length: 4 +Appending count: 25139 length: 5 +Appending count: 49667 length: 1 +Appending count: 14175 length: 9 +Appending count: 12251 length: 6 +Appending count: 8117 length: 8 +Appending count: 49229 length: 6 +Appending count: 22522 length: 3 +Appending count: 6974 length: 1 +Appending count: 20937 length: 6 +Appending count: 39142 length: 7 +Appending count: 12703 length: 9 +Appending count: 31700 length: 5 +Appending count: 44127 length: 8 +Appending count: 13304 length: 7 +Appending count: 34531 length: 8 +Appending count: 1265 length: 2 +Appending count: 42273 length: 1 +Appending count: 34740 length: 3 +Appending count: 11829 length: 2 +Appending count: 4837 length: 8 +Appending count: 29920 length: 10 +Appending count: 14293 length: 10 + position= 0 count= 38443 + position= 1 count= 38443 + position= 2 count= 38443 + position= 3 count= 22996 + position= 4 count= 22996 + position= 5 count= 22996 + position= 6 count= 22996 + position= 7 count= 22996 + position= 8 count= 22996 + position= 9 count= 22651 + position= 10 count= 22651 + position= 11 count= 22651 + position= 12 count= 22651 + position= 13 count= 22651 + position= 14 count= 22651 + position= 15 count= 22651 + position= 16 count= 22651 + position= 17 count= 22651 + position= 18 count= 22651 + position= 19 count= 44478 + position= 20 count= 44478 + position= 21 count= 44478 + position= 22 count= 44478 + position= 23 count= 44478 + position= 24 count= 44478 + position= 25 count= 44478 + position= 26 count= 31150 + position= 27 count= 31150 + position= 28 count= 31150 + position= 29 count= 31150 + position= 30 count= 31150 + position= 31 count= 31150 + position= 32 count= 31150 + position= 33 count= 31150 + position= 34 count= 31150 + position= 35 count= 43500 + position= 36 count= 30469 + position= 37 count= 30469 + position= 38 count= 30469 + position= 39 count= 30469 + position= 40 count= 16769 + position= 41 count= 16769 + position= 42 count= 16769 + position= 43 count= 16769 + position= 44 count= 25139 + position= 45 count= 25139 + position= 46 count= 25139 + position= 47 count= 25139 + position= 48 count= 25139 + position= 49 count= 49667 + position= 50 count= 14175 + position= 51 count= 14175 + position= 52 count= 14175 + position= 53 count= 14175 + position= 54 count= 14175 + position= 55 count= 14175 + position= 56 count= 14175 + position= 57 count= 14175 + position= 58 count= 14175 + position= 59 count= 12251 + position= 60 count= 12251 + position= 61 count= 12251 + position= 62 count= 12251 + position= 63 count= 12251 + position= 64 count= 12251 + position= 65 count= 8117 + position= 66 count= 8117 + position= 67 count= 8117 + position= 68 count= 8117 + position= 69 count= 8117 + position= 70 count= 8117 + position= 71 count= 8117 + position= 72 count= 8117 + position= 73 count= 49229 + position= 74 count= 49229 + position= 75 count= 49229 + position= 76 count= 49229 + position= 77 count= 49229 + position= 78 count= 49229 + position= 79 count= 22522 + position= 80 count= 22522 + position= 81 count= 22522 + position= 82 count= 6974 + position= 83 count= 20937 + position= 84 count= 20937 + position= 85 count= 20937 + position= 86 count= 20937 + position= 87 count= 20937 + position= 88 count= 20937 + position= 89 count= 39142 + position= 90 count= 39142 + position= 91 count= 39142 + position= 92 count= 39142 + position= 93 count= 39142 + position= 94 count= 39142 + position= 95 count= 39142 + position= 96 count= 12703 + position= 97 count= 12703 + position= 98 count= 12703 + position= 99 count= 12703 + position= 100 count= 12703 + position= 101 count= 12703 + position= 102 count= 12703 + position= 103 count= 12703 + position= 104 count= 12703 + position= 105 count= 31700 + position= 106 count= 31700 + position= 107 count= 31700 + position= 108 count= 31700 + position= 109 count= 31700 + position= 110 count= 44127 + position= 111 count= 44127 + position= 112 count= 44127 + position= 113 count= 44127 + position= 114 count= 44127 + position= 115 count= 44127 + position= 116 count= 44127 + position= 117 count= 44127 + position= 118 count= 13304 + position= 119 count= 13304 + position= 120 count= 13304 + position= 121 count= 13304 + position= 122 count= 13304 + position= 123 count= 13304 + position= 124 count= 13304 + position= 125 count= 34531 + position= 126 count= 34531 + position= 127 count= 34531 + position= 128 count= 34531 + position= 129 count= 34531 + position= 130 count= 34531 + position= 131 count= 34531 + position= 132 count= 34531 + position= 133 count= 1265 + position= 134 count= 1265 + position= 135 count= 42273 + position= 136 count= 34740 + position= 137 count= 34740 + position= 138 count= 34740 + position= 139 count= 11829 + position= 140 count= 11829 + position= 141 count= 4837 + position= 142 count= 4837 + position= 143 count= 4837 + position= 144 count= 4837 + position= 145 count= 4837 + position= 146 count= 4837 + position= 147 count= 4837 + position= 148 count= 4837 + position= 149 count= 29920 + position= 150 count= 29920 + position= 151 count= 29920 + position= 152 count= 29920 + position= 153 count= 29920 + position= 154 count= 29920 + position= 155 count= 29920 + position= 156 count= 29920 + position= 157 count= 29920 + position= 158 count= 29920 + position= 159 count= 14293 + position= 160 count= 14293 + position= 161 count= 14293 + position= 162 count= 14293 + position= 163 count= 14293 + position= 164 count= 14293 + position= 165 count= 14293 + position= 166 count= 14293 + position= 167 count= 14293 + position= 168 count= 14293 +21:38:03.964 WARN MessageChunksWriter - Using chunk-size=9 +21:38:04.010 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 +21:38:04.056 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 +21:38:04.105 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 -01:39:01.716 INFO RLoggerMainLoopCallback - R version 4.3.2 (2023-10-31) -- "Eye Holes" +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 +21:38:50.440 INFO RLoggerMainLoopCallback - + +21:38:50.442 INFO RLoggerMainLoopCallback - R version 4.3.2 (2023-10-31) -- "Eye Holes" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) -01:39:01.716 INFO RLoggerMainLoopCallback - R is free software and comes with ABSOLUTELY NO WARRANTY. +21:38:50.447 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. -01:39:01.717 INFO RLoggerMainLoopCallback - R is a collaborative project with many contributors. +21:38:50.448 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. -01:39:01.717 INFO RLoggerMainLoopCallback - Type 'demo()' for some demos, 'help()' for on-line help, or +21:38:50.448 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. -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] -01:39:01.913 WARN MessageChunksWriter - Using chunk-size=10000 -01:39:01.939 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.013 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.017 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.047 WARN MessageChunksWriter - Using chunk-size=1000 +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 +21:38:59.208 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 +21:38:59.282 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 +21:38:59.333 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 +21:38:59.386 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 +21:38:59.406 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 +21:38:59.422 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 +21:38:59.445 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 +21:38:59.457 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 +21:38:59.482 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 +21:38:59.509 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 +21:39:00.833 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 +21:39:00.847 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 +21:39:00.851 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 +21:39:00.853 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 +21:39:00.861 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 +21:39:00.869 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 +21:39:00.896 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 +21:39:00.909 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 +21:39:00.921 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 +21:39:00.937 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 +21:39:01.646 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 +21:39:01.666 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 +21:39:01.681 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 +21:39:01.693 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 +21:39:01.706 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 +21:39:01.731 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 +21:39:01.748 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 +21:39:01.765 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 +21:39:01.782 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 +21:39:01.820 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 +21:39:03.437 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen0.tmh has no 'too many hits' information (test-results/discover-variants/basen0.tmh does not exist). Assuming no queries have too many hits. +[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 +21:39:03.477 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 +21:39:03.515 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 +21:39:03.548 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 +21:39:03.577 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 +21:39:03.606 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 +21:39:03.647 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 +21:39:03.670 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 +21:39:03.714 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 +21:39:03.776 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 +21:39:05.207 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 +21:39:05.224 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 +21:39:05.244 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 +21:39:05.275 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 +21:39:05.315 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 +21:39:05.356 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 +21:39:05.397 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 +21:39:05.434 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 +21:39:05.492 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 +21:39:05.533 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 +21:39:06.393 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 +21:39:06.423 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 +21:39:06.462 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 +21:39:06.482 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 +21:39:06.517 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 +21:39:06.583 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 +21:39:06.614 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 +21:39:06.637 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 +21:39:06.668 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 +21:39:06.704 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 +21:39:07.730 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 +21:39:07.769 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 +21:39:07.786 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 +21:39:07.819 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 +21:39:07.849 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 +21:39:07.880 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 +21:39:07.949 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 +21:39:08.006 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 +21:39:08.047 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 +21:39:08.106 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 +21:39:08.845 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 +21:39:08.858 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 +21:39:08.869 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 +21:39:08.876 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 +21:39:08.882 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 +21:39:08.903 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 +21:39:08.909 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 +21:39:08.921 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 +21:39:08.930 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 +21:39:08.935 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 +21:39:09.189 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 +21:39:09.193 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 +21:39:09.200 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 +21:39:09.208 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 +21:39:09.224 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 +21:39:09.232 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 +21:39:09.240 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 +21:39:09.258 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 +21:39:09.266 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 +21:39:09.276 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 +21:39:10.313 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 +21:39:10.365 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 +21:39:10.396 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 +21:39:10.417 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 +21:39:10.457 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 +21:39:10.510 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 +21:39:10.534 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 +21:39:10.574 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 +21:39:10.609 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 +21:39:10.648 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 +21:39:12.093 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 +21:39:12.108 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 +21:39:12.133 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 +21:39:12.184 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 +21:39:12.193 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 +21:39:12.197 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 +21:39:12.200 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 +21:39:12.203 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 +21:39:12.211 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 +21:39:12.216 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 +21:39:12.855 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 +21:39:12.873 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 +21:39:12.900 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 +21:39:12.913 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 +21:39:12.919 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 +21:39:12.936 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 +21:39:12.950 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 +21:39:12.954 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 +21:39:12.979 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 +21:39:12.987 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 +21:39:20.582 INFO BullardUpperQuartileNormalization - normalization denominator 51939.5 for sample B-7 +21:39:20.583 INFO BullardUpperQuartileNormalization - normalization denominator 52838.6 for sample B-3 +21:39:20.583 INFO BullardUpperQuartileNormalization - normalization denominator 100421 for sample A-3 +21:39:20.583 INFO BullardUpperQuartileNormalization - normalization denominator 103257 for sample A-12 +21:39:20.583 INFO BullardUpperQuartileNormalization - normalization denominator 51455.4 for sample B-15 +21:39:20.584 INFO BullardUpperQuartileNormalization - normalization denominator 51662.8 for sample B-14 +21:39:20.584 INFO BullardUpperQuartileNormalization - normalization denominator 51455.4 for sample B-11 +21:39:20.595 INFO BullardUpperQuartileNormalization - normalization denominator 104571 for sample A-17 +21:39:20.596 INFO BullardUpperQuartileNormalization - normalization denominator 52285.3 for sample B-2 +21:39:20.596 INFO BullardUpperQuartileNormalization - normalization denominator 51317.0 for sample B-10 +21:39:20.596 INFO BullardUpperQuartileNormalization - normalization denominator 103326 for sample A-16 +21:39:20.596 INFO BullardUpperQuartileNormalization - normalization denominator 51593.7 for sample B-8 +21:39:20.596 INFO BullardUpperQuartileNormalization - normalization denominator 52976.9 for sample B-4 +21:39:20.596 INFO BullardUpperQuartileNormalization - normalization denominator 101251 for sample A-2 +21:39:20.597 INFO BullardUpperQuartileNormalization - normalization denominator 104294 for sample A-0 +21:39:20.597 INFO BullardUpperQuartileNormalization - normalization denominator 52285.3 for sample B-6 +21:39:20.597 INFO BullardUpperQuartileNormalization - normalization denominator 103948 for sample A-9 +21:39:20.597 INFO BullardUpperQuartileNormalization - normalization denominator 103326 for sample A-8 +21:39:20.597 INFO BullardUpperQuartileNormalization - normalization denominator 105193 for sample A-5 +21:39:20.597 INFO BullardUpperQuartileNormalization - normalization denominator 104363 for sample A-4 +21:39:20.597 INFO BullardUpperQuartileNormalization - normalization denominator 103533 for sample A-6 +21:39:20.597 INFO BullardUpperQuartileNormalization - normalization denominator 103464 for sample A-7 +21:39:20.598 INFO BullardUpperQuartileNormalization - normalization denominator 50487.1 for sample B-5 +21:39:20.598 INFO BullardUpperQuartileNormalization - normalization denominator 102980 for sample A-10 +21:39:20.598 INFO BullardUpperQuartileNormalization - normalization denominator 103118 for sample A-14 +21:39:20.598 INFO BullardUpperQuartileNormalization - normalization denominator 52631.1 for sample B-9 +21:39:20.598 INFO BullardUpperQuartileNormalization - normalization denominator 104086 for sample A-1 +21:39:20.603 INFO BullardUpperQuartileNormalization - normalization denominator 51455.4 for sample B-0 +21:39:20.603 INFO BullardUpperQuartileNormalization - normalization denominator 52077.8 for sample B-12 +21:39:20.603 INFO BullardUpperQuartileNormalization - normalization denominator 51109.6 for sample B-13 +21:39:20.603 INFO BullardUpperQuartileNormalization - normalization denominator 104640 for sample A-19 +21:39:20.604 INFO BullardUpperQuartileNormalization - normalization denominator 102980 for sample A-18 +21:39:20.604 INFO BullardUpperQuartileNormalization - normalization denominator 105331 for sample A-15 +21:39:20.604 INFO BullardUpperQuartileNormalization - normalization denominator 51732.0 for sample B-1 +21:39:20.604 INFO BullardUpperQuartileNormalization - normalization denominator 103671 for sample A-13 +21:39:20.604 INFO BullardUpperQuartileNormalization - normalization denominator 104017 for sample A-11 +21:39:20.604 INFO BullardUpperQuartileNormalization - normalization denominator 53115.2 for sample B-16 +21:39:20.604 INFO BullardUpperQuartileNormalization - normalization denominator 52631.1 for sample B-17 +21:39:20.604 INFO BullardUpperQuartileNormalization - normalization denominator 49933.8 for sample B-19 +21:39:20.605 INFO BullardUpperQuartileNormalization - normalization denominator 50418.0 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 + +21:39:21.073 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +21:39:21.420 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +21:39:21.420 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +21:39:21.572 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +21:39:21.573 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value +21:39:23.039 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. +21:39:23.353 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. +21:39:23.367 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value +21:39:24.675 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. +21:39:24.805 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 [0.9980727752766853, 0.49833720493874606, -0.0027830802237515445, -1.0048058078879458, 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 20 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 threads. +[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 20 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. +21:44:15.800 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:16.073 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:16.088 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:16.995 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:39:02.079 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.081 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.098 WARN GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent. -01:39:02.109 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. -01:39:02.165 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. -01:39:02.165 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. +21:44:17.086 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:17.089 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:17.113 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. +21:44:17.306 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. +21:44:17.307 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 -01:39:02.166 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. +21:44:17.308 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. [main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 7ms; used/avail/free/total/max mem: 55.98M/21.03G/1.30G/1.36G/21.09G -01:39:02.209 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: 6ms; used/avail/free/total/max mem: 388.29M/20.77G/182.13M/570.43M/21.16G +21:44:17.330 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 @@ -6460,36 +8173,36 @@ multiplicity: 1 query_length: 35 -01:39:02.305 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. -01:39:02.310 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. -01:39:02.362 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. -01:39:02.362 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. -01:39:02.362 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. -01:39:02.363 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. +21:44:17.480 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. +21:44:17.489 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. +21:44:17.669 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. +21:44:17.669 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. +21:44:17.669 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. +21:44:17.670 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 -01:39:02.363 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. -01:39:02.363 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. +21:44:17.670 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. +21:44:17.670 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: 48.85M/21.04G/1.31G/1.36G/21.09G -01:39:02.368 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. -01:39:02.384 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. -01:39:02.419 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.444 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.446 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.470 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 445.59M/20.71G/124.83M/570.43M/21.16G +21:44:17.683 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. +21:44:17.760 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/align-101.tmh has no 'too many hits' information (test-results/alignments/merge/align-101.tmh does not exist). Assuming no queries have too many hits. +21:44:17.952 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:18.075 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:18.097 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:18.401 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:39:02.494 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.496 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:18.692 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:18.707 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: 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 [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 141.13M/20.95G/1.22G/1.36G/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: 91.19M/21.06G/479.24M/570.43M/21.16G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -6618,25 +8331,25 @@ multiplicity: 1 query_length: 35 -01:39:02.622 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.648 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.650 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.673 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:19.637 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:19.928 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:19.944 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:20.131 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:39:02.696 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.697 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.700 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. -01:39:02.718 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. -01:39:02.719 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. +21:44:20.489 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:20.493 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:20.531 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. +21:44:20.577 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. +21:44:20.578 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 -01:39:02.719 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. +21:44:20.581 INFO AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item] +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 3ms [1 items, 500.00 items/s, 2.00 ms/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass Warning: could not find depth/max-length-of-match in too many hits information. [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 41.46M/21.05G/1.32G/1.36G/21.09G -01:39:02.722 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: 6ms; used/avail/free/total/max mem: 153.30M/21.00G/417.13M/570.43M/21.16G +21:44:20.598 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 @@ -6662,64 +8375,64 @@ multiplicity: 1 query_length: 35 -01:39:02.734 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.757 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.758 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.782 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:20.624 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:20.744 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:20.753 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:20.852 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:39:02.806 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.807 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.810 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. -01:39:02.812 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. -01:39:02.815 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. -01:39:02.816 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. -01:39:02.816 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. -01:39:02.816 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. +21:44:21.106 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:21.118 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:21.141 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. +21:44:21.153 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. +21:44:21.192 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. +21:44:21.192 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. +21:44:21.192 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. +21:44:21.192 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 -01:39:02.816 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. -01:39:02.816 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. +21:44:21.193 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. +21:44:21.193 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 - 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: 65.37M/21.02G/219.84M/285.21M/21.09G -01:39:02.819 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. -01:39:02.821 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. -01:39:02.826 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.850 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.851 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.875 WARN MessageChunksWriter - Using chunk-size=1000 +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 2ms; used/avail/free/total/max mem: 181.05M/20.98G/389.38M/570.43M/21.16G +21:44:21.206 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. +21:44:21.230 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. +21:44:21.257 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:21.461 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:21.497 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:22.048 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:39:02.899 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.900 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:22.345 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:22.362 WARN MessageChunksWriter - Using chunk-size=1000 Finding max number of reads... Found input file with 2 target(s) -01:39:02.902 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. +21:44:22.393 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) -01:39:02.905 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. +21:44:22.404 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. -01:39:02.908 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. -01:39:02.908 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. -01:39:02.908 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. -01:39:02.908 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. +21:44:22.436 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. +21:44:22.437 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. +21:44:22.437 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. +21:44:22.437 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 -01:39:02.909 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. -01:39:02.909 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. +21:44:22.437 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. +21:44:22.437 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: 98.93M/20.99G/186.29M/285.21M/21.09G +[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 14ms; used/avail/free/total/max mem: 203.79M/20.95G/366.64M/570.43M/21.16G Second pass: writing the merged alignment. -01:39:02.911 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. -01:39:02.913 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. +21:44:22.468 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. +21:44:22.481 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 @@ -6729,25 +8442,25 @@ Number of queries: 10 Number of targets: 4 Percent aligned: 100.0 -01:39:02.918 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.942 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.943 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.967 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:22.537 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:22.768 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:22.781 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:22.982 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:39:02.989 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.990 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:02.993 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. -01:39:02.995 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. -01:39:02.995 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. +21:44:23.333 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:23.362 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:23.405 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. +21:44:23.456 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. +21:44:23.456 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. [main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass -01:39:02.995 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. +21:44:23.457 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: 132.48M/20.96G/152.73M/285.21M/21.09G -01:39:02.998 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: 2ms; used/avail/free/total/max mem: 231.38M/20.92G/339.04M/570.43M/21.16G +21:44:23.505 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 @@ -6828,19 +8541,19 @@ multiplicity: 1 query_length: 35 -01:39:03.004 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.027 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.029 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.052 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:23.613 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:23.987 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:24.041 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:24.276 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:39:03.075 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.076 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:24.615 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:24.640 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 - Elapsed: 2ms [2 items, 2,000.00 items/s, 500.00 ?s/item] [main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass [main] INFO org.campagnelab.goby.alignments.Merge - Completed. -[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 182.81M/20.91G/102.40M/285.21M/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: 287.54M/20.87G/282.89M/570.43M/21.16G found entry: query_index: 2 target_index: 1999 position: 19993 @@ -6969,30 +8682,30 @@ multiplicity: 1 query_length: 35 -01:39:03.181 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.215 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.217 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.242 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:25.362 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:25.416 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:25.421 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:25.471 WARN MessageChunksWriter - Using chunk-size=1000 preparing 105 -01:39:03.265 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.267 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.271 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. -01:39:03.274 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. -01:39:03.302 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. -01:39:03.302 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. -01:39:03.302 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. -01:39:03.303 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. +21:44:25.745 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:25.776 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:25.817 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. +21:44:25.876 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. +21:44:26.401 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. +21:44:26.401 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. +21:44:26.401 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. +21:44:26.401 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 -01:39:03.303 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. -01:39:03.303 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. +21:44:26.402 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. +21:44:26.402 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: 108.40M/20.98G/696.91M/805.31M/21.09G -01:39:03.306 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. -01:39:03.320 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: 1ms; used/avail/free/total/max mem: 64.28M/21.09G/506.14M/570.43M/21.16G +21:44:26.445 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. +21:44:26.929 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 @@ -7153,7 +8866,7 @@ multiplicity: 1 query_length: 35 -01:39:03.571 WARN MessageChunksWriter - Using chunk-size=2 +21:44:27.647 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 0 Total bytes written: 31 Average bytes/logical entry: Infinity @@ -7162,7 +8875,7 @@ Number of queries: 2 Number of targets: 0 97 -01:39:03.580 WARN MessageChunksWriter - Using chunk-size=2 +21:44:27.708 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -7170,7 +8883,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:39:03.598 WARN MessageChunksWriter - Using chunk-size=2 +21:44:27.778 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -7178,7 +8891,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:39:03.601 WARN MessageChunksWriter - Using chunk-size=2 +21:44:27.838 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -7186,7 +8899,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:39:03.604 WARN MessageChunksWriter - Using chunk-size=2 +21:44:27.894 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 6 Total bytes written: 162 Average bytes/logical entry: 27.0 @@ -7194,34 +8907,69 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -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 - -01:39:03.662 WARN MessageChunksWriter - Using chunk-size=1000 +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 +21:44:28.021 WARN MessageChunksWriter - Using chunk-size=1000 +Setting quality threshold to 0.02 +21:44:28.108 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.164 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 +21:44:28.281 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.285 WARN MessageChunksWriter - Using chunk-size=1000 +entry: score=30.0000 readOriginIndex=0 +entry: score=30.0000 readOriginIndex=0 +Scanned 2 entries +21:44:28.363 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.388 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.485 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.508 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.600 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.633 WARN MessageChunksWriter - Using chunk-size=1000 +0 +2 +21:44:28.754 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.774 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 +21:44:28.879 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.916 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:28.994 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:29.027 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:29.124 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:29.144 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 @@ -7297,145 +9045,7 @@ read_index: 20 } -01:39:03.683 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 -01:39:03.762 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.765 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 -01:39:03.772 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.773 WARN MessageChunksWriter - Using chunk-size=1000 -entry: score=30.0000 readOriginIndex=0 -entry: score=30.0000 readOriginIndex=0 -Scanned 2 entries -01:39:03.777 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.778 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.783 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.784 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.789 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.790 WARN MessageChunksWriter - Using chunk-size=1000 -0 -2 -01:39:03.796 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.798 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 -01:39:03.804 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.805 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.836 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.837 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.842 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.843 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' -01:39:03.889 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.890 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.890 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.898 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.899 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.900 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.907 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.908 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.909 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 -01:39:03.916 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.917 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.918 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.924 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.925 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.926 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.928 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 -01:39:03.929 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 -01:39:03.931 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 -01:39:03.934 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.935 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.936 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:03.948 WARN MessageChunksWriter - Using chunk-size=1 -01:39:03.952 WARN MessageChunksWriter - Using chunk-size=1 -01:39:03.955 WARN MessageChunksWriter - Using chunk-size=1 -01:39:03.958 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. -01:39:03.986 WARN MessageChunksWriter - Using chunk-size=2 +21:44:29.671 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -7443,7 +9053,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:39:03.989 WARN MessageChunksWriter - Using chunk-size=2 +21:44:29.737 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -7451,7 +9061,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:39:03.991 WARN MessageChunksWriter - Using chunk-size=2 +21:44:29.819 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -7459,7 +9069,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:39:03.994 WARN MessageChunksWriter - Using chunk-size=2 +21:44:29.888 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -7467,7 +9077,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:39:03.997 WARN MessageChunksWriter - Using chunk-size=2 +21:44:29.948 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -7475,7 +9085,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:39:03.999 WARN MessageChunksWriter - Using chunk-size=2 +21:44:30.029 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -7483,7 +9093,7 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -01:39:04.002 WARN MessageChunksWriter - Using chunk-size=2 +21:44:30.093 WARN MessageChunksWriter - Using chunk-size=2 Total logical entries written: 7 Total bytes written: 219 Average bytes/logical entry: 31.285715 @@ -7491,1663 +9101,123 @@ Max query index: 0 Number of queries: 1 Number of targets: 3 -Setting quality threshold to 0.02 -01:39:04.028 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:04.030 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:04.037 WARN MessageChunksWriter - Using chunk-size=1000 -01:39:04.038 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.164 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.167 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.178 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.218 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.235 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.238 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.296 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.305 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.348 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 +21:44:30.470 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.485 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.488 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.570 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.635 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.638 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.658 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 +21:44:30.671 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 +21:44:30.673 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 +21:44:30.706 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.736 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.760 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.827 WARN MessageChunksWriter - Using chunk-size=1 +21:44:30.866 WARN MessageChunksWriter - Using chunk-size=1 +21:44:30.908 WARN MessageChunksWriter - Using chunk-size=1 +21:44:30.913 WARN MessageChunksWriter - Using chunk-size=1 +21:44:30.957 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:30.973 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:31.025 WARN MessageChunksWriter - Using chunk-size=1000 +21:44:32.017 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 -01:39:53.644 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 -01:39:53.644 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds -01:39:53.697 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -01:39:53.730 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -01:39:53.730 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -01:39:53.742 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -01:39:53.742 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value -01:39:53.833 INFO FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed. -01:39:53.860 INFO FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed. -01:39:53.860 INFO FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value -01:39:53.937 INFO FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed. -01:39:53.946 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 [0.9968909711873614, 0.49875859218382285, -0.00449236752427049, -1.003586399829636, 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 - -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 44190.5 for sample B-7 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 44249.6 for sample B-3 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 89150.0 for sample A-3 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 90155.7 for sample A-12 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 45018.7 for sample B-15 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 44722.9 for sample B-14 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 43717.2 for sample B-11 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 86192.2 for sample A-17 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 43894.7 for sample B-2 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 44486.3 for sample B-10 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 88262.7 for sample A-16 -01:40:05.917 INFO BullardUpperQuartileNormalization - normalization denominator 43658.1 for sample B-8 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 44013.0 for sample B-4 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 87020.4 for sample A-2 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 89800.8 for sample A-0 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 44131.3 for sample B-6 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 87848.6 for sample A-9 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 88262.7 for sample A-8 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 89623.3 for sample A-5 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 85364.0 for sample A-4 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 89386.7 for sample A-6 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 91989.6 for sample A-7 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 44013.0 for sample B-5 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 89090.9 for sample A-10 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 88972.6 for sample A-14 -01:40:05.918 INFO BullardUpperQuartileNormalization - normalization denominator 44841.2 for sample B-9 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 87848.6 for sample A-1 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 43598.9 for sample B-0 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 44486.3 for sample B-12 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 43717.2 for sample B-13 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 89268.3 for sample A-19 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 87138.7 for sample A-18 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 87552.8 for sample A-15 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 43362.3 for sample B-1 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 85364.0 for sample A-13 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 90688.1 for sample A-11 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 44308.8 for sample B-16 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 45610.3 for sample B-17 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 42948.2 for sample B-19 -01:40:05.919 INFO BullardUpperQuartileNormalization - normalization denominator 43717.2 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: 14977972 -score: 780.0 +position: 0 +query_position: 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 -} +query_length: 75 +query_aligned_length: 75 +target_aligned_length: 75 +mapping_quality: 255 +pair_flags: 0 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 -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 +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 -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 -01:40:07.122 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 -01:40:07.123 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 -01:40:07.124 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 -01:40:07.125 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 -01:40:07.126 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 -01:40:07.128 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 -01:40:07.129 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 -01:40:07.130 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 -01:40:07.131 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 -01:40:07.132 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 -01:40:07.191 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 -01:40:07.192 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 -01:40:07.193 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 -01:40:07.194 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 -01:40:07.195 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 -01:40:07.196 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 -01:40:07.198 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 -01:40:07.199 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 -01:40:07.200 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 -01:40:07.201 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 -01:40:07.258 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 -01:40:07.259 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 -01:40:07.260 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 -01:40:07.261 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 -01:40:07.261 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 -01:40:07.262 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 -01:40:07.263 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 -01:40:07.264 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 -01:40:07.265 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 -01:40:07.266 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 -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 -01:40:07.320 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 -01:40:07.321 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 -01:40:07.322 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 -01:40:07.323 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 -01:40:07.324 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 -01:40:07.325 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 -01:40:07.326 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 -01:40:07.327 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 -01:40:07.328 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 -01:40:07.329 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 -01:40:07.374 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 -01:40:07.375 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 -01:40:07.376 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 -01:40:07.377 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 -01:40:07.378 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 -01:40:07.379 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 -01:40:07.379 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 -01:40:07.380 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 -01:40:07.382 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 -01:40:07.383 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 -01:40:07.425 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 -01:40:07.426 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 -01:40:07.427 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 -01:40:07.428 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 -01:40:07.429 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 -01:40:07.430 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 -01:40:07.431 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 -01:40:07.432 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 -01:40:07.433 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 -01:40:07.434 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 -01:40:07.507 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 -01:40:07.508 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 -01:40:07.509 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 -01:40:07.510 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 -01:40:07.511 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 -01:40:07.512 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 -01:40:07.513 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 -01:40:07.514 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 -01:40:07.515 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 -01:40:07.516 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 -01:40:07.556 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 -01:40:07.557 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 -01:40:07.558 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 -01:40:07.559 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 -01:40:07.559 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 -01:40:07.560 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 -01:40:07.562 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 -01:40:07.563 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 -01:40:07.564 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 -01:40:07.565 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 -01:40:07.604 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 -01:40:07.605 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 -01:40:07.606 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 -01:40:07.606 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 -01:40:07.607 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 -01:40:07.608 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 -01:40:07.609 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 -01:40:07.610 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 -01:40:07.611 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 -01:40:07.612 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 -01:40:07.650 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 -01:40:07.651 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 -01:40:07.652 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 -01:40:07.653 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 -01:40:07.654 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 -01:40:07.654 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 -01:40:07.655 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 -01:40:07.656 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 -01:40:07.657 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 -01:40:07.659 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 -01:40:07.698 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 -01:40:07.699 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 -01:40:07.700 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 -01:40:07.701 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 -01:40:07.702 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 -01:40:07.703 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 -01:40:07.703 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 -01:40:07.704 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 -01:40:07.705 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 -01:40:07.706 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 -01:40:07.749 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 -01:40:07.750 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 -01:40:07.751 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 -01:40:07.752 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 -01:40:07.753 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 -01:40:07.754 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 -01:40:07.755 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 -01:40:07.756 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 -01:40:07.757 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 -01:40:07.758 INFO AlignmentTooManyHitsReader - basename test-results/discover-variants/basen9.tmh has no 'too many hits' information (test-results/discover-variants/basen9.tmh does not exist). Assuming no queries have too many hits. -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - start reading TMH for test-results/discover-variants/basen9 -[main] INFO org.campagnelab.goby.alignments.NonAmbiguousAlignmentReader - done reading TMH for test-results/discover-variants/basen9 -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 +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' +21:44:32.345 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: 0 -Number of queries: 1 -Number of targets: 45 +Max query index: 1999 +Number of queries: 2000 +Number of targets: 10 +21:44:33.283 INFO TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0 +21:44:33.283 INFO TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT - 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: 33146 length: 9 -Appending count: 5977 length: 10 -Appending count: 10235 length: 3 -Appending count: 45889 length: 5 -Appending count: 8549 length: 6 -Appending count: 23174 length: 4 -Appending count: 20325 length: 6 -Appending count: 6351 length: 1 -Appending count: 15289 length: 10 -Appending count: 15856 length: 2 -Appending count: 46337 length: 5 -Appending count: 10299 length: 1 -Appending count: 18671 length: 2 -Appending count: 28742 length: 1 -Appending count: 13037 length: 1 -Appending count: 7432 length: 2 -Appending count: 10861 length: 6 -Appending count: 22908 length: 9 -Appending count: 24507 length: 4 -Appending count: 30184 length: 5 -Appending count: 13791 length: 5 -Appending count: 32696 length: 6 -Appending count: 21151 length: 2 -Appending count: 17331 length: 10 -Appending count: 20498 length: 2 -Appending count: 13904 length: 1 -Appending count: 16479 length: 7 -Appending count: 1361 length: 3 -Appending count: 33299 length: 5 -Appending count: 10460 length: 2 - position= 0 count= 33146 - position= 1 count= 33146 - position= 2 count= 33146 - position= 3 count= 33146 - position= 4 count= 33146 - position= 5 count= 33146 - position= 6 count= 33146 - position= 7 count= 33146 - position= 8 count= 33146 - position= 9 count= 5977 - position= 10 count= 5977 - position= 11 count= 5977 - position= 12 count= 5977 - position= 13 count= 5977 - position= 14 count= 5977 - position= 15 count= 5977 - position= 16 count= 5977 - position= 17 count= 5977 - position= 18 count= 5977 - position= 19 count= 10235 - position= 20 count= 10235 - position= 21 count= 10235 - position= 22 count= 45889 - position= 23 count= 45889 - position= 24 count= 45889 - position= 25 count= 45889 - position= 26 count= 45889 - position= 27 count= 8549 - position= 28 count= 8549 - position= 29 count= 8549 - position= 30 count= 8549 - position= 31 count= 8549 - position= 32 count= 8549 - position= 33 count= 23174 - position= 34 count= 23174 - position= 35 count= 23174 - position= 36 count= 23174 - position= 37 count= 20325 - position= 38 count= 20325 - position= 39 count= 20325 - position= 40 count= 20325 - position= 41 count= 20325 - position= 42 count= 20325 - position= 43 count= 6351 - position= 44 count= 15289 - position= 45 count= 15289 - position= 46 count= 15289 - position= 47 count= 15289 - position= 48 count= 15289 - position= 49 count= 15289 - position= 50 count= 15289 - position= 51 count= 15289 - position= 52 count= 15289 - position= 53 count= 15289 - position= 54 count= 15856 - position= 55 count= 15856 - position= 56 count= 46337 - position= 57 count= 46337 - position= 58 count= 46337 - position= 59 count= 46337 - position= 60 count= 46337 - position= 61 count= 10299 - position= 62 count= 18671 - position= 63 count= 18671 - position= 64 count= 28742 - position= 65 count= 13037 - position= 66 count= 7432 - position= 67 count= 7432 - position= 68 count= 10861 - position= 69 count= 10861 - position= 70 count= 10861 - position= 71 count= 10861 - position= 72 count= 10861 - position= 73 count= 10861 - position= 74 count= 22908 - position= 75 count= 22908 - position= 76 count= 22908 - position= 77 count= 22908 - position= 78 count= 22908 - position= 79 count= 22908 - position= 80 count= 22908 - position= 81 count= 22908 - position= 82 count= 22908 - position= 83 count= 24507 - position= 84 count= 24507 - position= 85 count= 24507 - position= 86 count= 24507 - position= 87 count= 30184 - position= 88 count= 30184 - position= 89 count= 30184 - position= 90 count= 30184 - position= 91 count= 30184 - position= 92 count= 13791 - position= 93 count= 13791 - position= 94 count= 13791 - position= 95 count= 13791 - position= 96 count= 13791 - position= 97 count= 32696 - position= 98 count= 32696 - position= 99 count= 32696 - position= 100 count= 32696 - position= 101 count= 32696 - position= 102 count= 32696 - position= 103 count= 21151 - position= 104 count= 21151 - position= 105 count= 17331 - position= 106 count= 17331 - position= 107 count= 17331 - position= 108 count= 17331 - position= 109 count= 17331 - position= 110 count= 17331 - position= 111 count= 17331 - position= 112 count= 17331 - position= 113 count= 17331 - position= 114 count= 17331 - position= 115 count= 20498 - position= 116 count= 20498 - position= 117 count= 13904 - position= 118 count= 16479 - position= 119 count= 16479 - position= 120 count= 16479 - position= 121 count= 16479 - position= 122 count= 16479 - position= 123 count= 16479 - position= 124 count= 16479 - position= 125 count= 1361 - position= 126 count= 1361 - position= 127 count= 1361 - position= 128 count= 33299 - position= 129 count= 33299 - position= 130 count= 33299 - position= 131 count= 33299 - position= 132 count= 33299 - position= 133 count= 10460 - position= 134 count= 10460 - peak : start :5 count :13 length :100010 - peak : start :100020 count :10 length :1 -01:40:08.181 WARN WiggleWindow - Not writing 101 7 -01:40:08.181 WARN WiggleWindow - Not writing 111 7 -01:40:08.181 WARN WiggleWindow - Not writing 131 8 -01:40:08.181 WARN WiggleWindow - Not writing 141 8 -01:40:08.181 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 -AGC01:40:08.265 WARN MessageChunksWriter - Using chunk-size=9 -01:40:08.266 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 -01:40:08.268 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 -01:40:08.270 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: 71.055 s - in TestSuite -01:40:12.083 INFO GobyRengine - Shutdown hook is terminating R +[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 636.259 s - in TestSuite +21:44:42.583 INFO GobyRengine - Shutdown hook is terminating R [INFO] [INFO] Results: [INFO] @@ -9156,14 +9226,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.036 s] -[INFO] Goby I/O ........................................... SUCCESS [ 5.597 s] -[INFO] Goby Full Distribution ............................. SUCCESS [01:24 min] +[INFO] Goby Framework ..................................... SUCCESS [ 0.247 s] +[INFO] Goby I/O ........................................... SUCCESS [ 57.980 s] +[INFO] Goby Full Distribution ............................. SUCCESS [11:30 min] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 01:29 min -[INFO] Finished at: 2025-06-09T01:40:20-12:00 +[INFO] Total time: 12:29 min +[INFO] Finished at: 2024-05-07T21:44:51+14:00 [INFO] ------------------------------------------------------------------------ make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2' create-stamp debian/debhelper-build-stamp @@ -9231,14 +9301,14 @@ [INFO] ------------------------------------------------------------------------ [INFO] Reactor Summary for Goby Framework 3.3.1: [INFO] -[INFO] Goby Framework ..................................... SUCCESS [ 0.292 s] -[INFO] Goby I/O ........................................... SUCCESS [ 0.177 s] -[INFO] Goby Full Distribution ............................. SUCCESS [ 0.030 s] +[INFO] Goby Framework ..................................... SUCCESS [ 3.599 s] +[INFO] Goby I/O ........................................... SUCCESS [ 0.782 s] +[INFO] Goby Full Distribution ............................. SUCCESS [ 0.868 s] [INFO] ------------------------------------------------------------------------ [INFO] BUILD SUCCESS [INFO] ------------------------------------------------------------------------ -[INFO] Total time: 0.618 s -[INFO] Finished at: 2025-06-09T01:40:22-12:00 +[INFO] Total time: 6.625 s +[INFO] Finished at: 2024-05-07T21:45:17+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... @@ -9249,12 +9319,12 @@ > 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 -Jun 09, 2025 1:40:28 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +May 07, 2024 9:45:37 PM org.debian.maven.packager.DependenciesSolver$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 -Jun 09, 2025 1:40:33 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve +May 07, 2024 9:45:43 PM org.debian.maven.packager.DependenciesSolver$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 @@ -9299,12 +9369,14 @@ 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/4155971/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/4155971/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/89880 and its subdirectories -I: Current time: Mon Jun 9 01:40:46 -12 2025 -I: pbuilder-time-stamp: 1749476446 +I: removing directory /srv/workspace/pbuilder/4155971 and its subdirectories +I: Current time: Tue May 7 21:47:24 +14 2024 +I: pbuilder-time-stamp: 1715068044