I: pbuilder: network access will be disabled during build
I: Current time: Fri Feb 14 02:27:50 +14 2025
I: pbuilder-time-stamp: 1739449670
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [libgoby-java_3.3.1+dfsg2-9.dsc]
I: copying [./libgoby-java_3.3.1+dfsg2.orig.tar.xz]
I: copying [./libgoby-java_3.3.1+dfsg2-9.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Nov 19 06:09:52 2022 
gpgv:                using RSA key 33CB284313E90BD27DCB4523600316A6DC277476
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./libgoby-java_3.3.1+dfsg2-9.dsc: no acceptable signature found
dpkg-source: info: extracting libgoby-java in libgoby-java-3.3.1+dfsg2
dpkg-source: info: unpacking libgoby-java_3.3.1+dfsg2.orig.tar.xz
dpkg-source: info: unpacking libgoby-java_3.3.1+dfsg2-9.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying protoc.patch
dpkg-source: info: applying adding_dependencies.patch
dpkg-source: info: applying using_jbzip2.patch
dpkg-source: info: applying adapting_to_old_fastutil.patch
dpkg-source: info: applying using_GeneratedMessageV3.patch
dpkg-source: info: applying using_commons-cli.patch
dpkg-source: info: applying using_correct_SamReader_api.patch
dpkg-source: info: applying inclusions_in_SplitTranscriptsMode.patch
dpkg-source: info: applying catch_IOException_LineIterator.patch
dpkg-source: info: applying computing_fisher_pvalue_hypergeom.patch
dpkg-source: info: applying exclude_not_runnable_tests.patch
dpkg-source: info: applying goby_script.patch
dpkg-source: info: applying path_of_goby_jar_for_Debian.patch
dpkg-source: info: applying jaxb_dependency.patch
dpkg-source: info: applying using_pcre2.patch
dpkg-source: info: applying omit_test_failing_randomly.patch
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/2185384/tmp/hooks/D01_modify_environment starting
debug: Running on ionos5-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 Feb 13 12:27 /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/2185384/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/2185384/tmp/hooks/D02_print_environment starting
I: set
  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]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu")
  BASH_VERSION='5.2.15(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=16 '
  DIRSTACK=()
  DISTRIBUTION=bookworm
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=x86_64
  HOST_ARCH=amd64
  IFS=' 	
  '
  INVOCATION_ID=90f07de72062449cbc72b85daf4d0efc
  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=2185384
  PS4='+ '
  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.g7IW0ol2/pbuilderrc_1NPu --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.g7IW0ol2/b2 --logfile b2/build.log libgoby-java_3.3.1+dfsg2-9.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://85.184.249.68:3128
I: uname -a
  Linux i-capture-the-hostname 6.5.0-0.deb12.4-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.5.10-1~bpo12+1 (2023-11-23) x86_64 GNU/Linux
I: ls -l /bin
  total 5632
  -rwxr-xr-x 1 root root 1265648 Apr 23  2023 bash
  -rwxr-xr-x 3 root root   39224 Sep 19  2022 bunzip2
  -rwxr-xr-x 3 root root   39224 Sep 19  2022 bzcat
  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzcmp -> bzdiff
  -rwxr-xr-x 1 root root    2225 Sep 19  2022 bzdiff
  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzegrep -> bzgrep
  -rwxr-xr-x 1 root root    4893 Nov 27  2021 bzexe
  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzfgrep -> bzgrep
  -rwxr-xr-x 1 root root    3775 Sep 19  2022 bzgrep
  -rwxr-xr-x 3 root root   39224 Sep 19  2022 bzip2
  -rwxr-xr-x 1 root root   14568 Sep 19  2022 bzip2recover
  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzless -> bzmore
  -rwxr-xr-x 1 root root    1297 Sep 19  2022 bzmore
  -rwxr-xr-x 1 root root   44016 Sep 20  2022 cat
  -rwxr-xr-x 1 root root   68656 Sep 20  2022 chgrp
  -rwxr-xr-x 1 root root   64496 Sep 20  2022 chmod
  -rwxr-xr-x 1 root root   72752 Sep 20  2022 chown
  -rwxr-xr-x 1 root root  151152 Sep 20  2022 cp
  -rwxr-xr-x 1 root root  125640 Jan  5  2023 dash
  -rwxr-xr-x 1 root root  121904 Sep 20  2022 date
  -rwxr-xr-x 1 root root   89240 Sep 20  2022 dd
  -rwxr-xr-x 1 root root  102200 Sep 20  2022 df
  -rwxr-xr-x 1 root root  151344 Sep 20  2022 dir
  -rwxr-xr-x 1 root root   88656 Mar 23  2023 dmesg
  lrwxrwxrwx 1 root root       8 Dec 19  2022 dnsdomainname -> hostname
  lrwxrwxrwx 1 root root       8 Dec 19  2022 domainname -> hostname
  -rwxr-xr-x 1 root root   43856 Sep 20  2022 echo
  -rwxr-xr-x 1 root root      41 Jan 24  2023 egrep
  -rwxr-xr-x 1 root root   35664 Sep 20  2022 false
  -rwxr-xr-x 1 root root      41 Jan 24  2023 fgrep
  -rwxr-xr-x 1 root root   85600 Mar 23  2023 findmnt
  -rwsr-xr-x 1 root root   35128 Mar 23  2023 fusermount
  -rwxr-xr-x 1 root root  203152 Jan 24  2023 grep
  -rwxr-xr-x 2 root root    2346 Apr 10  2022 gunzip
  -rwxr-xr-x 1 root root    6447 Apr 10  2022 gzexe
  -rwxr-xr-x 1 root root   98136 Apr 10  2022 gzip
  -rwxr-xr-x 1 root root   22680 Dec 19  2022 hostname
  -rwxr-xr-x 1 root root   72824 Sep 20  2022 ln
  -rwxr-xr-x 1 root root   53024 Mar 23  2023 login
  -rwxr-xr-x 1 root root  151344 Sep 20  2022 ls
  -rwxr-xr-x 1 root root  207168 Mar 23  2023 lsblk
  -rwxr-xr-x 1 root root   97552 Sep 20  2022 mkdir
  -rwxr-xr-x 1 root root   72912 Sep 20  2022 mknod
  -rwxr-xr-x 1 root root   43952 Sep 20  2022 mktemp
  -rwxr-xr-x 1 root root   59712 Mar 23  2023 more
  -rwsr-xr-x 1 root root   59704 Mar 23  2023 mount
  -rwxr-xr-x 1 root root   18744 Mar 23  2023 mountpoint
  -rwxr-xr-x 1 root root  142968 Sep 20  2022 mv
  lrwxrwxrwx 1 root root       8 Dec 19  2022 nisdomainname -> hostname
  lrwxrwxrwx 1 root root      14 Apr  3  2023 pidof -> /sbin/killall5
  -rwxr-xr-x 1 root root   43952 Sep 20  2022 pwd
  lrwxrwxrwx 1 root root       4 Apr 23  2023 rbash -> bash
  -rwxr-xr-x 1 root root   52112 Sep 20  2022 readlink
  -rwxr-xr-x 1 root root   72752 Sep 20  2022 rm
  -rwxr-xr-x 1 root root   56240 Sep 20  2022 rmdir
  -rwxr-xr-x 1 root root   27560 Jul 28  2023 run-parts
  -rwxr-xr-x 1 root root  126424 Jan  5  2023 sed
  lrwxrwxrwx 1 root root       9 Feb 13 12:27 sh -> /bin/bash
  -rwxr-xr-x 1 root root   43888 Sep 20  2022 sleep
  -rwxr-xr-x 1 root root   85008 Sep 20  2022 stty
  -rwsr-xr-x 1 root root   72000 Mar 23  2023 su
  -rwxr-xr-x 1 root root   39824 Sep 20  2022 sync
  -rwxr-xr-x 1 root root  531984 Apr  6  2023 tar
  -rwxr-xr-x 1 root root   14520 Jul 28  2023 tempfile
  -rwxr-xr-x 1 root root  109616 Sep 20  2022 touch
  -rwxr-xr-x 1 root root   35664 Sep 20  2022 true
  -rwxr-xr-x 1 root root   14568 Mar 23  2023 ulockmgr_server
  -rwsr-xr-x 1 root root   35128 Mar 23  2023 umount
  -rwxr-xr-x 1 root root   43888 Sep 20  2022 uname
  -rwxr-xr-x 2 root root    2346 Apr 10  2022 uncompress
  -rwxr-xr-x 1 root root  151344 Sep 20  2022 vdir
  -rwxr-xr-x 1 root root   72024 Mar 23  2023 wdctl
  lrwxrwxrwx 1 root root       8 Dec 19  2022 ypdomainname -> hostname
  -rwxr-xr-x 1 root root    1984 Apr 10  2022 zcat
  -rwxr-xr-x 1 root root    1678 Apr 10  2022 zcmp
  -rwxr-xr-x 1 root root    6460 Apr 10  2022 zdiff
  -rwxr-xr-x 1 root root      29 Apr 10  2022 zegrep
  -rwxr-xr-x 1 root root      29 Apr 10  2022 zfgrep
  -rwxr-xr-x 1 root root    2081 Apr 10  2022 zforce
  -rwxr-xr-x 1 root root    8103 Apr 10  2022 zgrep
  -rwxr-xr-x 1 root root    2206 Apr 10  2022 zless
  -rwxr-xr-x 1 root root    1842 Apr 10  2022 zmore
  -rwxr-xr-x 1 root root    4577 Apr 10  2022 znew
I: user script /srv/workspace/pbuilder/2185384/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), maven-debian-helper, javahelper, default-jdk, ant, ant-contrib, libjbzip2-java, libcommons-collections3-java, libcommons-configuration-java, libcommons-exec-java, libcommons-io-java, libcommons-lang-java, libcommons-logging-java, libcommons-math-java, libcommons-cli-java, libdistlib-java, liblog4j1.2-java, libexec-maven-plugin-java, libjaxb-api-java, libmaven-assembly-plugin-java, libmaven-antrun-plugin-java, libbuild-helper-maven-plugin-java, libmaven-dependency-plugin-java, libmaven-source-plugin-java, libmaven-javadoc-plugin-java, libprotobuf-java, libhtsjdk-java, libfastutil-java, protobuf-compiler, libjsap-java, libdsiutils-java, libicb-utils-java, libreflections-java, libpj-java, libprotobuf-dev, pkg-config, r-cran-rjava, libeasymock-java, junit4, testng, libpicard-java
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 18148 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on maven-debian-helper; however:
  Package maven-debian-helper is not installed.
 pbuilder-satisfydepends-dummy depends on javahelper; however:
  Package javahelper is not installed.
 pbuilder-satisfydepends-dummy depends on default-jdk; however:
  Package default-jdk is not installed.
 pbuilder-satisfydepends-dummy depends on ant; however:
  Package ant is not installed.
 pbuilder-satisfydepends-dummy depends on ant-contrib; however:
  Package ant-contrib is not installed.
 pbuilder-satisfydepends-dummy depends on libjbzip2-java; however:
  Package libjbzip2-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-collections3-java; however:
  Package libcommons-collections3-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-configuration-java; however:
  Package libcommons-configuration-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-exec-java; however:
  Package libcommons-exec-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-io-java; however:
  Package libcommons-io-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-lang-java; however:
  Package libcommons-lang-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-logging-java; however:
  Package libcommons-logging-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-math-java; however:
  Package libcommons-math-java is not installed.
 pbuilder-satisfydepends-dummy depends on libcommons-cli-java; however:
  Package libcommons-cli-java is not installed.
 pbuilder-satisfydepends-dummy depends on libdistlib-java; however:
  Package libdistlib-java is not installed.
 pbuilder-satisfydepends-dummy depends on liblog4j1.2-java; however:
  Package liblog4j1.2-java is not installed.
 pbuilder-satisfydepends-dummy depends on libexec-maven-plugin-java; however:
  Package libexec-maven-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libjaxb-api-java; however:
  Package libjaxb-api-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-assembly-plugin-java; however:
  Package libmaven-assembly-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-antrun-plugin-java; however:
  Package libmaven-antrun-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libbuild-helper-maven-plugin-java; however:
  Package libbuild-helper-maven-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-dependency-plugin-java; however:
  Package libmaven-dependency-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-source-plugin-java; however:
  Package libmaven-source-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libmaven-javadoc-plugin-java; however:
  Package libmaven-javadoc-plugin-java is not installed.
 pbuilder-satisfydepends-dummy depends on libprotobuf-java; however:
  Package libprotobuf-java is not installed.
 pbuilder-satisfydepends-dummy depends on libhtsjdk-java; however:
  Package libhtsjdk-java is not installed.
 pbuilder-satisfydepends-dummy depends on libfastutil-java; however:
  Package libfastutil-java is not installed.
 pbuilder-satisfydepends-dummy depends on protobuf-compiler; however:
  Package protobuf-compiler is not installed.
 pbuilder-satisfydepends-dummy depends on libjsap-java; however:
  Package libjsap-java is not installed.
 pbuilder-satisfydepends-dummy depends on libdsiutils-java; however:
  Package libdsiutils-java is not installed.
 pbuilder-satisfydepends-dummy depends on libicb-utils-java; however:
  Package libicb-utils-java is not installed.
 pbuilder-satisfydepends-dummy depends on libreflections-java; however:
  Package libreflections-java is not installed.
 pbuilder-satisfydepends-dummy depends on libpj-java; however:
  Package libpj-java is not installed.
 pbuilder-satisfydepends-dummy depends on libprotobuf-dev; however:
  Package libprotobuf-dev is not installed.
 pbuilder-satisfydepends-dummy depends on pkg-config; however:
  Package pkg-config is not installed.
 pbuilder-satisfydepends-dummy depends on r-cran-rjava; however:
  Package r-cran-rjava is not installed.
 pbuilder-satisfydepends-dummy depends on libeasymock-java; however:
  Package libeasymock-java is not installed.
 pbuilder-satisfydepends-dummy depends on junit4; however:
  Package junit4 is not installed.
 pbuilder-satisfydepends-dummy depends on testng; however:
  Package testng is not installed.
 pbuilder-satisfydepends-dummy depends on libpicard-java; however:
  Package libpicard-java is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  adwaita-icon-theme{a} ant{a} ant-contrib{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} dctrl-tools{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} devscripts{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dirmngr{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gnupg{a} gnupg-l10n{a} gnupg-utils{a} gpg{a} gpg-agent{a} gpg-wks-client{a} gpg-wks-server{a} gpgconf{a} gpgsm{a} groff-base{a} gtk-update-icon-cache{a} hicolor-icon-theme{a} intltool-debian{a} java-common{a} java-wrappers{a} javahelper{a} junit4{a} junit5{a} libactivation-java{a} libaopalliance-java{a} libapache-pom-java{a} libapiguardian-java{a} libarchive-zip-perl{a} libasm-java{a} libasound2{a} libasound2-data{a} libassuan0{a} libatinject-jsr330-api-java{a} libatk1.0-0{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libb-hooks-op-check-perl{a} libbarclay-java{a} libbatik-java{a} libblas3{a} libbrotli1{a} libbsd0{a} libbsh-java{a} libbuild-helper-maven-plugin-java{a} libbyte-buddy-java{a} libcairo2{a} libcdi-api-java{a} libclass-method-modifiers-perl{a} libclass-xsaccessor-perl{a} libclone-perl{a} libcolt-free-java{a} libcommons-beanutils-java{a} libcommons-cli-java{a} libcommons-codec-java{a} libcommons-collections3-java{a} libcommons-collections4-java{a} libcommons-compress-java{a} libcommons-configuration-java{a} libcommons-digester-java{a} libcommons-exec-java{a} libcommons-io-java{a} libcommons-jexl2-java{a} libcommons-lang-java{a} libcommons-lang3-java{a} libcommons-logging-java{a} libcommons-math-java{a} libcommons-math3-java{a} libcommons-parent-java{a} libcommons-text-java{a} libcommons-validator-java{a} libconcurrent-java{a} libcups2{a} libcurl4{a} libdatrie1{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate0{a} libdevel-callchecker-perl{a} libdistlib-java{a} libdom4j-java{a} libdoxia-core-java{a} libdoxia-java{a} libdoxia-sitetools-java{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libdsiutils-java{a} libdynaloader-functions-perl{a} libeasymock-java{a} libedit2{a} libel-api-java{a} libelf1{a} libencode-locale-perl{a} liberror-prone-java{a} libexec-maven-plugin-java{a} libexpat1{a} libfastutil-java{a} libfile-dirlist-perl{a} libfile-homedir-perl{a} libfile-listing-perl{a} libfile-stripnondeterminism-perl{a} libfile-touch-perl{a} libfile-which-perl{a} libfontbox2-java{a} libfontconfig1{a} libfop-java{a} libfreemarker-java{a} libfreetype6{a} libfribidi0{a} libgatk-native-bindings-java{a} libgdk-pixbuf-2.0-0{a} libgdk-pixbuf2.0-common{a} libgeronimo-annotation-1.3-spec-java{a} libgeronimo-interceptor-3.0-spec-java{a} libgfortran5{a} libgif7{a} libgkl-java{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglvnd0{a} libglx-mesa0{a} libglx0{a} libgoogle-gson-java{a} libgraphite2-3{a} libgtk2.0-0{a} libgtk2.0-common{a} libguava-java{a} libguice-java{a} libhamcrest-java{a} libharfbuzz0b{a} libhtml-parser-perl{a} libhtml-tagset-perl{a} libhtml-tree-perl{a} libhtsjdk-java{a} libhttp-cookies-perl{a} libhttp-date-perl{a} libhttp-message-perl{a} libhttp-negotiate-perl{a} libhttpclient-java{a} libhttpcore-java{a} libicb-utils-java{a} libice6{a} libicu4j-java{a} libicu72{a} libimport-into-perl{a} libio-html-perl{a} libio-pty-perl{a} libio-socket-ssl-perl{a} libipc-run-perl{a} libitext1-java{a} libjansi-java{a} libjavassist-java{a} libjaxb-api-java{a} libjaxen-java{a} libjaxp1.3-java{a} libjbig0{a} libjboss-logging-java{a} libjboss-vfs-java{a} libjbzip2-java{a} libjcommander-java{a} libjetty9-java{a} libjoptsimple-java{a} libjpeg62-turbo{a} libjsap-java{a} libjsoup-java{a} libjsp-api-java{a} libjsr305-java{a} libjtidy-java{a} libksba8{a} liblapack3{a} liblcms2-2{a} libldap-2.5-0{a} liblerc4{a} liblightcouch-java{a} libllvm15{a} liblog4j1.2-java{a} liblog4j2-java{a} liblogback-java{a} liblwp-mediatypes-perl{a} liblwp-protocol-https-perl{a} libmagic-mgc{a} libmagic1{a} libmaven-antrun-plugin-java{a} libmaven-archiver-java{a} libmaven-artifact-transfer-java{a} libmaven-assembly-plugin-java{a} libmaven-clean-plugin-java{a} libmaven-common-artifact-filters-java{a} libmaven-compiler-plugin-java{a} libmaven-dependency-analyzer-java{a} libmaven-dependency-plugin-java{a} libmaven-dependency-tree-java{a} libmaven-file-management-java{a} libmaven-filtering-java{a} libmaven-invoker-java{a} libmaven-jar-plugin-java{a} libmaven-javadoc-plugin-java{a} libmaven-parent-java{a} libmaven-plugin-tools-java{a} libmaven-reporting-api-java{a} libmaven-reporting-exec-java{a} libmaven-reporting-impl-java{a} libmaven-resolver-java{a} libmaven-resources-plugin-java{a} libmaven-shared-incremental-java{a} libmaven-shared-io-java{a} libmaven-shared-utils-java{a} libmaven-site-plugin-java{a} libmaven-source-plugin-java{a} libmaven3-core-java{a} libmbedcrypto7{a} libmbedtls14{a} libmbedx509-1{a} libmjson-java{a} libmodule-runtime-perl{a} libmongodb-java{a} libmoo-perl{a} libncbi-ngs3{a} libncbi-vdb3{a} libnet-http-perl{a} libnet-ssleay-perl{a} libnghttp2-14{a} libngs-java{a} libngs-jni{a} libnpth0{a} libnspr4{a} libnss3{a} libobjenesis-java{a} libopentest4j-java{a} libopentest4j-reporting-java{a} liboro-java{a} libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libparams-classify-perl{a} libpciaccess0{a} libpcsclite1{a} libpicard-java{a} libpicocli-java{a} libpipeline1{a} libpixman-1-0{a} libpj-java{a} libpkgconf3{a} libplexus-ant-factory-java{a} libplexus-archiver-java{a} libplexus-bsh-factory-java{a} libplexus-build-api-java{a} libplexus-cipher-java{a} libplexus-classworlds-java{a} libplexus-compiler-java{a} libplexus-component-annotations-java{a} libplexus-container-default-java{a} libplexus-container-default1.5-java{a} libplexus-i18n-java{a} libplexus-interactivity-api-java{a} libplexus-interpolation-java{a} libplexus-io-java{a} libplexus-languages-java{a} libplexus-sec-dispatcher-java{a} libplexus-utils2-java{a} libplexus-velocity-java{a} libpng16-16{a} libproc2-0{a} libprotobuf-dev{a} libprotobuf-java{a} libprotobuf-lite32{a} libprotobuf32{a} libprotoc32{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqdox-java{a} libqdox2-java{a} libreadline8{a} libreflections-java{a} libregexp-ipv6-perl{a} librhino-java{a} librole-tiny-perl{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libservlet-api-java{a} libsisu-inject-java{a} libsisu-plexus-java{a} libslf4j-java{a} libsm6{a} libsnappy-java{a} libsnappy-jni{a} libsnappy1v5{a} libssh2-1{a} libsub-override-perl{a} libsub-quote-perl{a} libsurefire-java{a} libtcl8.6{a} libthai-data{a} libthai0{a} libtiff6{a} libtimedate-perl{a} libtk8.6{a} libtool{a} libtry-tiny-perl{a} libuchardet0{a} libunivocity-parsers-java{a} liburi-perl{a} libvelocity-tools-java{a} libwagon-file-java{a} libwagon-http-shaded-java{a} libwagon-provider-api-java{a} libwebp7{a} libwebsocket-api-java{a} libwww-perl{a} libwww-robotrules-perl{a} libx11-6{a} libx11-data{a} libx11-xcb1{a} libxalan2-java{a} libxau6{a} libxbean-reflect-java{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-xfixes0{a} libxcb1{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp6{a} libxerces2-java{a} libxext6{a} libxfixes3{a} libxft2{a} libxi6{a} libxinerama1{a} libxml-commons-external-java{a} libxml-commons-resolver1.1-java{a} libxml2{a} libxml2-utils{a} libxmlgraphics-commons-java{a} libxpp3-java{a} libxrandr2{a} libxrender1{a} libxshmfence1{a} libxss1{a} libxstream-java{a} libxt6{a} libxtst6{a} libxxf86vm1{a} libxz-java{a} libz3-4{a} m4{a} man-db{a} maven{a} maven-debian-helper{a} maven-repo-helper{a} media-types{a} ncbi-vdb-data{a} netbase{a} openjdk-17-jdk{a} openjdk-17-jdk-headless{a} openjdk-17-jre{a} openjdk-17-jre-headless{a} openssl{a} patchutils{a} perl-openssl-defaults{a} pinentry-curses{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} protobuf-compiler{a} python3{a} python3-minimal{a} python3.11{a} python3.11-minimal{a} r-base-core{a} r-cran-rjava{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} testng{a} tzdata{a} ucf{a} unzip{a} velocity{a} wdiff{a} x11-common{a} xdg-utils{a} zip{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  alsa-topology-conf alsa-ucm-conf ant-optional curl dbus debian-keyring dput dput-ng dupload equivs fonts-dejavu-extra icc-profiles-free libarchive-cpio-perl libatk-wrapper-java-jni libdata-dump-perl libdistlib-java-doc libdistro-info-perl libfile-mimeinfo-perl libgail-common libgdk-pixbuf2.0-bin libgit-wrapper-perl libgitlab-api-v4-perl libgkl-jni libglib2.0-data libgtk2.0-bin libhtml-form-perl libhtml-format-perl libhttp-daemon-perl libldap-common liblist-compare-perl libltdl-dev libmail-sendmail-perl libmailtools-perl libnamespace-clean-perl libnet-dbus-perl librsvg2-common libsasl2-modules libsaxon-java libsoap-lite-perl libstring-shellquote-perl libx11-protocol-perl libxstring-perl libxt-dev libyaml-snake-java licensecheck lintian lynx pristine-tar psmisc publicsuffix python3-apt python3-debian python3-magic python3-requests python3-unidiff python3-xdg r-base-dev r-doc-html r-recommended strace wget x11-utils x11-xserver-utils xdg-user-dirs 
0 packages upgraded, 430 newly installed, 0 to remove and 0 not upgraded.
Need to get 381 MB of archives. After unpacking 932 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB]
Get: 2 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB]
Get: 3 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB]
Get: 4 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get: 8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB]
Get: 9 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B]
Get: 11 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB]
Get: 12 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB]
Get: 13 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2023c-5+deb12u1 [296 kB]
Get: 14 http://deb.debian.org/debian bookworm/main amd64 netbase all 6.4 [12.8 kB]
Get: 15 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB]
Get: 16 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB]
Get: 17 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 18 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB]
Get: 19 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB]
Get: 20 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB]
Get: 21 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB]
Get: 22 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB]
Get: 23 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB]
Get: 24 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get: 25 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB]
Get: 26 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB]
Get: 27 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get: 28 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB]
Get: 29 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB]
Get: 30 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB]
Get: 31 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB]
Get: 32 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB]
Get: 33 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get: 34 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB]
Get: 35 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB]
Get: 36 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB]
Get: 37 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB]
Get: 38 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB]
Get: 39 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB]
Get: 40 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB]
Get: 41 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB]
Get: 42 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB]
Get: 43 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB]
Get: 44 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.38-2~deb12u1 [44.0 kB]
Get: 45 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB]
Get: 46 http://deb.debian.org/debian bookworm/main amd64 ca-certificates-java all 20230710~deb12u1 [11.9 kB]
Get: 47 http://deb.debian.org/debian bookworm/main amd64 java-common all 0.74 [6388 B]
Get: 48 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB]
Get: 49 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB]
Get: 50 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.10-1~deb12u1 [201 kB]
Get: 51 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB]
Get: 52 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3+deb12u5 [245 kB]
Get: 53 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB]
Get: 54 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB]
Get: 55 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB]
Get: 56 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB]
Get: 57 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB]
Get: 58 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB]
Get: 59 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.35-1 [113 kB]
Get: 60 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.87.1-1 [1331 kB]
Get: 61 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.8-1 [20.5 kB]
Get: 62 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.8-1+b1 [362 kB]
Get: 63 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB]
Get: 64 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB]
Get: 65 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.9-2 [49.7 kB]
Get: 66 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre-headless amd64 17.0.9+9-1~deb12u1 [43.7 MB]
Get: 67 http://deb.debian.org/debian bookworm/main amd64 default-jre-headless amd64 2:1.17-74 [2936 B]
Get: 68 http://deb.debian.org/debian bookworm/main amd64 ant all 1.10.13-1 [2161 kB]
Get: 69 http://deb.debian.org/debian bookworm/main amd64 ant-contrib all 1.0~b3+svn177-12 [262 kB]
Get: 70 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB]
Get: 71 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB]
Get: 72 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB]
Get: 73 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get: 74 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get: 75 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB]
Get: 76 http://deb.debian.org/debian bookworm/main amd64 dctrl-tools amd64 2.24-3+b1 [104 kB]
Get: 77 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB]
Get: 78 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB]
Get: 79 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB]
Get: 80 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 81 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get: 82 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 83 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 84 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB]
Get: 85 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB]
Get: 86 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB]
Get: 87 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 88 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 89 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB]
Get: 90 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-common all 2.24.33-2 [2700 kB]
Get: 91 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB]
Get: 92 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB]
Get: 93 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB]
Get: 94 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB]
Get: 95 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB]
Get: 96 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB]
Get: 97 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB]
Get: 98 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB]
Get: 99 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB]
Get: 100 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB]
Get: 101 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB]
Get: 102 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB]
Get: 103 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB]
Get: 104 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB]
Get: 105 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB]
Get: 106 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB]
Get: 107 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB]
Get: 108 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB]
Get: 109 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB]
Get: 110 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB]
Get: 111 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB]
Get: 112 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB]
Get: 113 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB]
Get: 114 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB]
Get: 115 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB]
Get: 116 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB]
Get: 117 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB]
Get: 118 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB]
Get: 119 http://deb.debian.org/debian bookworm/main amd64 libgtk2.0-0 amd64 2.24.33-2 [1855 kB]
Get: 120 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB]
Get: 121 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B]
Get: 122 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB]
Get: 123 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB]
Get: 124 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2+deb12u2 [192 kB]
Get: 125 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB]
Get: 126 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB]
Get: 127 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB]
Get: 128 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB]
Get: 129 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB]
Get: 130 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB]
Get: 131 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB]
Get: 132 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B]
Get: 133 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB]
Get: 134 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB]
Get: 135 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB]
Get: 136 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB]
Get: 137 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB]
Get: 138 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB]
Get: 139 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB]
Get: 140 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB]
Get: 141 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB]
Get: 142 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB]
Get: 143 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB]
Get: 144 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB]
Get: 145 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB]
Get: 146 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB]
Get: 147 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB]
Get: 148 http://deb.debian.org/debian bookworm/main amd64 libgif7 amd64 5.2.1-2.5 [46.9 kB]
Get: 149 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB]
Get: 150 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB]
Get: 151 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jre amd64 17.0.9+9-1~deb12u1 [184 kB]
Get: 152 http://deb.debian.org/debian bookworm/main amd64 default-jre amd64 2:1.17-74 [1056 B]
Get: 153 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk-headless amd64 17.0.9+9-1~deb12u1 [71.3 MB]
Get: 154 http://deb.debian.org/debian bookworm/main amd64 default-jdk-headless amd64 2:1.17-74 [1108 B]
Get: 155 http://deb.debian.org/debian bookworm/main amd64 openjdk-17-jdk amd64 17.0.9+9-1~deb12u1 [2777 kB]
Get: 156 http://deb.debian.org/debian bookworm/main amd64 default-jdk amd64 2:1.17-74 [1068 B]
Get: 157 http://deb.debian.org/debian bookworm/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB]
Get: 158 http://deb.debian.org/debian bookworm/main amd64 gpgconf amd64 2.2.40-1.1 [564 kB]
Get: 159 http://deb.debian.org/debian bookworm/main amd64 libksba8 amd64 1.6.3-2 [128 kB]
Get: 160 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB]
Get: 161 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB]
Get: 162 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB]
Get: 163 http://deb.debian.org/debian bookworm/main amd64 libnpth0 amd64 1.6-3 [19.0 kB]
Get: 164 http://deb.debian.org/debian bookworm/main amd64 dirmngr amd64 2.2.40-1.1 [792 kB]
Get: 165 http://deb.debian.org/debian bookworm/main amd64 gnupg-l10n all 2.2.40-1.1 [1093 kB]
Get: 166 http://deb.debian.org/debian bookworm/main amd64 gnupg-utils amd64 2.2.40-1.1 [927 kB]
Get: 167 http://deb.debian.org/debian bookworm/main amd64 gpg amd64 2.2.40-1.1 [949 kB]
Get: 168 http://deb.debian.org/debian bookworm/main amd64 pinentry-curses amd64 1.2.1-1 [77.4 kB]
Get: 169 http://deb.debian.org/debian bookworm/main amd64 gpg-agent amd64 2.2.40-1.1 [695 kB]
Get: 170 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-client amd64 2.2.40-1.1 [541 kB]
Get: 171 http://deb.debian.org/debian bookworm/main amd64 gpg-wks-server amd64 2.2.40-1.1 [531 kB]
Get: 172 http://deb.debian.org/debian bookworm/main amd64 gpgsm amd64 2.2.40-1.1 [671 kB]
Get: 173 http://deb.debian.org/debian bookworm/main amd64 gnupg all 2.2.40-1.1 [846 kB]
Get: 174 http://deb.debian.org/debian bookworm/main amd64 libfile-dirlist-perl all 0.05-3 [7600 B]
Get: 175 http://deb.debian.org/debian bookworm/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get: 176 http://deb.debian.org/debian bookworm/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get: 177 http://deb.debian.org/debian bookworm/main amd64 libfile-touch-perl all 0.12-2 [8816 B]
Get: 178 http://deb.debian.org/debian bookworm/main amd64 libio-pty-perl amd64 1:1.17-1 [34.9 kB]
Get: 179 http://deb.debian.org/debian bookworm/main amd64 libipc-run-perl all 20220807.0-1 [104 kB]
Get: 180 http://deb.debian.org/debian bookworm/main amd64 libclass-method-modifiers-perl all 2.14-1 [18.1 kB]
Get: 181 http://deb.debian.org/debian bookworm/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB]
Get: 182 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB]
Get: 183 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB]
Get: 184 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB]
Get: 185 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB]
Get: 186 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB]
Get: 187 http://deb.debian.org/debian bookworm/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB]
Get: 188 http://deb.debian.org/debian bookworm/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB]
Get: 189 http://deb.debian.org/debian bookworm/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB]
Get: 190 http://deb.debian.org/debian bookworm/main amd64 libmoo-perl all 2.005005-1 [58.0 kB]
Get: 191 http://deb.debian.org/debian bookworm/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB]
Get: 192 http://deb.debian.org/debian bookworm/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB]
Get: 193 http://deb.debian.org/debian bookworm/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB]
Get: 194 http://deb.debian.org/debian bookworm/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB]
Get: 195 http://deb.debian.org/debian bookworm/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB]
Get: 196 http://deb.debian.org/debian bookworm/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B]
Get: 197 http://deb.debian.org/debian bookworm/main amd64 liburi-perl all 5.17-1 [90.4 kB]
Get: 198 http://deb.debian.org/debian bookworm/main amd64 libhtml-parser-perl amd64 3.81-1 [101 kB]
Get: 199 http://deb.debian.org/debian bookworm/main amd64 libhtml-tree-perl all 5.07-3 [211 kB]
Get: 200 http://deb.debian.org/debian bookworm/main amd64 libclone-perl amd64 0.46-1 [13.7 kB]
Get: 201 http://deb.debian.org/debian bookworm/main amd64 libio-html-perl all 1.004-3 [16.2 kB]
Get: 202 http://deb.debian.org/debian bookworm/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB]
Get: 203 http://deb.debian.org/debian bookworm/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB]
Get: 204 http://deb.debian.org/debian bookworm/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB]
Get: 205 http://deb.debian.org/debian bookworm/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB]
Get: 206 http://deb.debian.org/debian bookworm/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B]
Get: 207 http://deb.debian.org/debian bookworm/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB]
Get: 208 http://deb.debian.org/debian bookworm/main amd64 libio-socket-ssl-perl all 2.081-2 [219 kB]
Get: 209 http://deb.debian.org/debian bookworm/main amd64 libnet-http-perl all 6.22-1 [25.3 kB]
Get: 210 http://deb.debian.org/debian bookworm/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB]
Get: 211 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB]
Get: 212 http://deb.debian.org/debian bookworm/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB]
Get: 213 http://deb.debian.org/debian bookworm/main amd64 libwww-perl all 6.68-1 [186 kB]
Get: 214 http://deb.debian.org/debian bookworm/main amd64 patchutils amd64 0.4.2-1 [77.5 kB]
Get: 215 http://deb.debian.org/debian bookworm/main amd64 wdiff amd64 1.2.2-5 [119 kB]
Get: 216 http://deb.debian.org/debian bookworm/main amd64 devscripts amd64 2.23.4+deb12u1 [1073 kB]
Get: 217 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB]
Get: 218 http://deb.debian.org/debian bookworm/main amd64 java-wrappers all 0.4 [8916 B]
Get: 219 http://deb.debian.org/debian bookworm/main amd64 javahelper all 0.78 [97.2 kB]
Get: 220 http://deb.debian.org/debian bookworm/main amd64 libhamcrest-java all 2.2-1 [121 kB]
Get: 221 http://deb.debian.org/debian bookworm/main amd64 junit4 all 4.13.2-3 [348 kB]
Get: 222 http://deb.debian.org/debian bookworm/main amd64 libapiguardian-java all 1.1.2-1 [4656 B]
Get: 223 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-java all 1.2.0-4 [9516 B]
Get: 224 http://deb.debian.org/debian bookworm/main amd64 libopentest4j-reporting-java all 0.1.0-M1-2 [49.0 kB]
Get: 225 http://deb.debian.org/debian bookworm/main amd64 libpicocli-java all 4.6.2-2 [390 kB]
Get: 226 http://deb.debian.org/debian bookworm/main amd64 libunivocity-parsers-java all 2.9.1-1 [397 kB]
Get: 227 http://deb.debian.org/debian bookworm/main amd64 junit5 all 5.9.2-1 [2398 kB]
Get: 228 http://deb.debian.org/debian bookworm/main amd64 libactivation-java all 1.2.0-2 [84.7 kB]
Get: 229 http://deb.debian.org/debian bookworm/main amd64 libaopalliance-java all 20070526-7 [8572 B]
Get: 230 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B]
Get: 231 http://deb.debian.org/debian bookworm/main amd64 libasm-java all 9.4-1 [389 kB]
Get: 232 http://deb.debian.org/debian bookworm/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B]
Get: 233 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB]
Get: 234 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang3-java all 3.12.0-2 [561 kB]
Get: 235 http://deb.debian.org/debian bookworm/main amd64 libfreemarker-java all 2.3.31-2 [1528 kB]
Get: 236 http://deb.debian.org/debian bookworm/main amd64 libgoogle-gson-java all 2.10-1 [261 kB]
Get: 237 http://deb.debian.org/debian bookworm/main amd64 libjoptsimple-java all 5.0.4-4 [73.1 kB]
Get: 238 http://deb.debian.org/debian bookworm/main amd64 libcommons-codec-java all 1.15-1 [292 kB]
Get: 239 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB]
Get: 240 http://deb.debian.org/debian bookworm/main amd64 libhttpcore-java all 4.4.16-1 [636 kB]
Get: 241 http://deb.debian.org/debian bookworm/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB]
Get: 242 http://deb.debian.org/debian bookworm/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB]
Get: 243 http://deb.debian.org/debian bookworm/main amd64 libmongodb-java all 3.6.3-2 [1901 kB]
Get: 244 http://deb.debian.org/debian bookworm/main amd64 libslf4j-java all 1.7.32-1 [144 kB]
Get: 245 http://deb.debian.org/debian bookworm/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB]
Get: 246 http://deb.debian.org/debian bookworm/main amd64 libbarclay-java all 4.1.0+dfsg-1 [103 kB]
Get: 247 http://deb.debian.org/debian bookworm/main amd64 libjaxp1.3-java all 1.3.05-6 [227 kB]
Get: 248 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-external-java all 1.4.01-5 [240 kB]
Get: 249 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB]
Get: 250 http://deb.debian.org/debian bookworm/main amd64 libxmlgraphics-commons-java all 2.8-2 [623 kB]
Get: 251 http://deb.debian.org/debian bookworm/main amd64 libbatik-java all 1.16+dfsg-1+deb12u1 [3949 kB]
Get: 252 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB]
Get: 253 http://deb.debian.org/debian bookworm/main amd64 libbsh-java all 2.0b4-20 [291 kB]
Get: 254 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-utils-java all 3.3.4-1 [138 kB]
Get: 255 http://deb.debian.org/debian bookworm/main amd64 libcommons-cli-java all 1.5.0-1 [60.0 kB]
Get: 256 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-annotation-1.3-spec-java all 1.3-1 [11.1 kB]
Get: 257 http://deb.debian.org/debian bookworm/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB]
Get: 258 http://deb.debian.org/debian bookworm/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB]
Get: 259 http://deb.debian.org/debian bookworm/main amd64 libguava-java all 31.1-1 [2613 kB]
Get: 260 http://deb.debian.org/debian bookworm/main amd64 libguice-java all 4.2.3-2 [1435 kB]
Get: 261 http://deb.debian.org/debian bookworm/main amd64 libmaven-parent-java all 35-1 [6140 B]
Get: 262 http://deb.debian.org/debian bookworm/main amd64 libplexus-utils2-java all 3.4.2-1 [258 kB]
Get: 263 http://deb.debian.org/debian bookworm/main amd64 libwagon-provider-api-java all 3.5.3-1 [48.2 kB]
Get: 264 http://deb.debian.org/debian bookworm/main amd64 libmaven-resolver-java all 1.6.3-1 [548 kB]
Get: 265 http://deb.debian.org/debian bookworm/main amd64 libplexus-cipher-java all 2.0-1 [14.9 kB]
Get: 266 http://deb.debian.org/debian bookworm/main amd64 libplexus-classworlds-java all 2.7.0-1 [50.6 kB]
Get: 267 http://deb.debian.org/debian bookworm/main amd64 libplexus-component-annotations-java all 2.1.1-1 [7660 B]
Get: 268 http://deb.debian.org/debian bookworm/main amd64 libplexus-interpolation-java all 1.26-1 [76.8 kB]
Get: 269 http://deb.debian.org/debian bookworm/main amd64 libplexus-sec-dispatcher-java all 2.0-3 [28.3 kB]
Get: 270 http://deb.debian.org/debian bookworm/main amd64 libgeronimo-interceptor-3.0-spec-java all 1.0.1-4 [8484 B]
Get: 271 http://deb.debian.org/debian bookworm/main amd64 libcdi-api-java all 1.2-3 [54.3 kB]
Get: 272 http://deb.debian.org/debian bookworm/main amd64 libsisu-inject-java all 0.3.4-2 [347 kB]
Get: 273 http://deb.debian.org/debian bookworm/main amd64 libsisu-plexus-java all 0.3.4-3 [181 kB]
Get: 274 http://deb.debian.org/debian bookworm/main amd64 libmaven3-core-java all 3.8.7-1 [1572 kB]
Get: 275 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-io-java all 3.0.0-4 [33.2 kB]
Get: 276 http://deb.debian.org/debian bookworm/main amd64 libmaven-file-management-java all 3.0.0-1 [35.1 kB]
Get: 277 http://deb.debian.org/debian bookworm/main amd64 libbuild-helper-maven-plugin-java all 3.3.0-1 [59.5 kB]
Get: 278 http://deb.debian.org/debian bookworm/main amd64 libbyte-buddy-java all 1.12.21-1 [4393 kB]
Get: 279 http://deb.debian.org/debian bookworm/main amd64 libconcurrent-java all 1.3.4-6 [140 kB]
Get: 280 http://deb.debian.org/debian bookworm/main amd64 libcolt-free-java all 1.2.0+dfsg-7 [434 kB]
Get: 281 http://deb.debian.org/debian bookworm/main amd64 libcommons-collections3-java all 3.2.2-2 [526 kB]
Get: 282 http://deb.debian.org/debian bookworm/main amd64 libcommons-beanutils-java all 1.9.4-1 [232 kB]
Get: 283 http://deb.debian.org/debian bookworm/main amd64 libcommons-collections4-java all 4.2-1 [662 kB]
Get: 284 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB]
Get: 285 http://deb.debian.org/debian bookworm/main amd64 libcommons-lang-java all 2.6-10 [273 kB]
Get: 286 http://deb.debian.org/debian bookworm/main amd64 libcommons-configuration-java all 1.10-6 [347 kB]
Get: 287 http://deb.debian.org/debian bookworm/main amd64 libcommons-digester-java all 1.8.1-5 [168 kB]
Get: 288 http://deb.debian.org/debian bookworm/main amd64 libcommons-exec-java all 1.3-2 [48.1 kB]
Get: 289 http://deb.debian.org/debian bookworm/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB]
Get: 290 http://deb.debian.org/debian bookworm/main amd64 libcommons-math-java all 2.2-8 [926 kB]
Get: 291 http://deb.debian.org/debian bookworm/main amd64 libcommons-math3-java all 3.6.1-3 [2018 kB]
Get: 292 http://deb.debian.org/debian bookworm/main amd64 libplexus-io-java all 3.3.1-2 [65.3 kB]
Get: 293 http://deb.debian.org/debian bookworm/main amd64 libsnappy1v5 amd64 1.1.9-3 [26.0 kB]
Get: 294 http://deb.debian.org/debian bookworm/main amd64 libsnappy-jni amd64 1.1.8.3-1 [7152 B]
Get: 295 http://deb.debian.org/debian bookworm/main amd64 libsnappy-java all 1.1.8.3-1 [98.9 kB]
Get: 296 http://deb.debian.org/debian bookworm/main amd64 libxz-java all 1.9-1 [143 kB]
Get: 297 http://deb.debian.org/debian bookworm/main amd64 libplexus-archiver-java all 4.6.1-1 [187 kB]
Get: 298 http://deb.debian.org/debian bookworm/main amd64 libmaven-archiver-java all 3.6.0-1 [25.1 kB]
Get: 299 http://deb.debian.org/debian bookworm/main amd64 libmaven-jar-plugin-java all 3.3.0-2 [24.0 kB]
Get: 300 http://deb.debian.org/debian bookworm/main amd64 libcommons-text-java all 1.10.0-1 [211 kB]
Get: 301 http://deb.debian.org/debian bookworm/main amd64 libcommons-validator-java all 1:1.7-1 [181 kB]
Get: 302 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB]
Get: 303 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB]
Get: 304 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB]
Get: 305 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB]
Get: 306 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u4 [390 kB]
Get: 307 http://deb.debian.org/debian bookworm/main amd64 libdistlib-java all 1.0-4 [72.1 kB]
Get: 308 http://deb.debian.org/debian bookworm/main amd64 libjaxen-java all 1.1.6-4 [214 kB]
Get: 309 http://deb.debian.org/debian bookworm/main amd64 libdom4j-java all 2.1.3-2 [310 kB]
Get: 310 http://deb.debian.org/debian bookworm/main amd64 libdoxia-core-java all 1.12.0-1 [213 kB]
Get: 311 http://deb.debian.org/debian bookworm/main amd64 libfontbox2-java all 2.0.27-2 [1510 kB]
Get: 312 http://deb.debian.org/debian bookworm/main amd64 libqdox-java all 1.12.1-3 [172 kB]
Get: 313 http://deb.debian.org/debian bookworm/main amd64 libfop-java all 1:2.8-2 [10.1 MB]
Get: 314 http://deb.debian.org/debian bookworm/main amd64 libitext1-java all 1.4-7 [1257 kB]
Get: 315 http://deb.debian.org/debian bookworm/main amd64 libxbean-reflect-java all 4.5-8 [133 kB]
Get: 316 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default-java all 2.1.1-1 [193 kB]
Get: 317 http://deb.debian.org/debian bookworm/main amd64 libdoxia-java all 1.12.0-1 [459 kB]
Get: 318 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-api-java all 3.1.1-1 [7240 B]
Get: 319 http://deb.debian.org/debian bookworm/main amd64 libplexus-i18n-java all 1.0-beta-10-6 [13.4 kB]
Get: 320 http://deb.debian.org/debian bookworm/main amd64 velocity all 1.7-6 [429 kB]
Get: 321 http://deb.debian.org/debian bookworm/main amd64 libplexus-velocity-java all 1.2-3.1 [10.5 kB]
Get: 322 http://deb.debian.org/debian bookworm/main amd64 liboro-java all 2.0.8a-14 [70.5 kB]
Get: 323 http://deb.debian.org/debian bookworm/main amd64 libvelocity-tools-java all 2.0-8 [308 kB]
Get: 324 http://deb.debian.org/debian bookworm/main amd64 libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB]
Get: 325 http://deb.debian.org/debian bookworm/main amd64 libxerces2-java all 2.12.2-1 [1440 kB]
Get: 326 http://deb.debian.org/debian bookworm/main amd64 libxalan2-java all 2.7.2-4 [3419 kB]
Get: 327 http://deb.debian.org/debian bookworm/main amd64 libdoxia-sitetools-java all 1.11.1-1 [202 kB]
Get: 328 http://deb.debian.org/debian bookworm/main amd64 libfastutil-java all 8.5.11+dfsg-1 [19.6 MB]
Get: 329 http://deb.debian.org/debian bookworm/main amd64 libxpp3-java all 1.1.4c-3 [292 kB]
Get: 330 http://deb.debian.org/debian bookworm/main amd64 libxstream-java all 1.4.20-1 [565 kB]
Get: 331 http://deb.debian.org/debian bookworm/main amd64 libjsap-java all 2.1-5 [102 kB]
Get: 332 http://deb.debian.org/debian bookworm/main amd64 liblogback-java all 1:1.2.11-3 [700 kB]
Get: 333 http://deb.debian.org/debian bookworm/main amd64 libdsiutils-java all 2.7.2+dfsg-1 [523 kB]
Get: 334 http://deb.debian.org/debian bookworm/main amd64 libobjenesis-java all 3.3-3 [41.3 kB]
Get: 335 http://deb.debian.org/debian bookworm/main amd64 libeasymock-java all 5.1.0-1 [129 kB]
Get: 336 http://deb.debian.org/debian bookworm/main amd64 libel-api-java all 3.0.0-3 [64.9 kB]
Get: 337 http://deb.debian.org/debian bookworm/main amd64 libexec-maven-plugin-java all 3.1.0-1 [66.2 kB]
Get: 338 http://deb.debian.org/debian bookworm/main amd64 libgatk-native-bindings-java all 1.0.0+dfsg-2 [8024 B]
Get: 339 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB]
Get: 340 http://deb.debian.org/debian bookworm/main amd64 libmjson-java all 1.4.0-3 [60.4 kB]
Get: 341 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB]
Get: 342 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB]
Get: 343 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB]
Get: 344 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB]
Get: 345 http://deb.debian.org/debian bookworm/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2 [1050 kB]
Get: 346 http://deb.debian.org/debian bookworm/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6~deb12u1 [154 kB]
Get: 347 http://deb.debian.org/debian bookworm/main amd64 libngs-jni amd64 3.0.3+dfsg-6~deb12u1 [23.5 kB]
Get: 348 http://deb.debian.org/debian bookworm/main amd64 libngs-java amd64 3.0.3+dfsg-6~deb12u1 [110 kB]
Get: 349 http://deb.debian.org/debian bookworm/main amd64 librhino-java all 1.7.14-2.1 [1357 kB]
Get: 350 http://deb.debian.org/debian bookworm/main amd64 libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB]
Get: 351 http://deb.debian.org/debian bookworm/main amd64 libgkl-java all 0.8.10+dfsg-3 [25.0 kB]
Get: 352 http://deb.debian.org/debian bookworm/main amd64 libicu4j-java all 72.1-1 [16.3 MB]
Get: 353 http://deb.debian.org/debian bookworm/main amd64 liblog4j1.2-java all 1.2.17-11 [444 kB]
Get: 354 http://deb.debian.org/debian bookworm/main amd64 libicb-utils-java all 2.0.1+git20161002.afee1d9-5 [81.5 kB]
Get: 355 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB]
Get: 356 http://deb.debian.org/debian bookworm/main amd64 libjansi-java all 2.4.0-2 [105 kB]
Get: 357 http://deb.debian.org/debian bookworm/main amd64 libjavassist-java all 1:3.27.0-1 [731 kB]
Get: 358 http://deb.debian.org/debian bookworm/main amd64 libjaxb-api-java all 2.3.1-1 [119 kB]
Get: 359 http://deb.debian.org/debian bookworm/main amd64 libjboss-logging-java all 3.5.0-2 [59.4 kB]
Get: 360 http://deb.debian.org/debian bookworm/main amd64 libjboss-vfs-java all 3.2.15.Final-2 [129 kB]
Get: 361 http://deb.debian.org/debian bookworm/main amd64 libjbzip2-java all 0.9.1-8 [42.7 kB]
Get: 362 http://deb.debian.org/debian bookworm/main amd64 libjcommander-java all 1.71-4 [73.0 kB]
Get: 363 http://deb.debian.org/debian bookworm/main amd64 libjsp-api-java all 2.3.4-3 [53.7 kB]
Get: 364 http://deb.debian.org/debian bookworm/main amd64 libservlet-api-java all 4.0.1-2 [81.0 kB]
Get: 365 http://deb.debian.org/debian bookworm/main amd64 libwebsocket-api-java all 1.1-2 [40.1 kB]
Get: 366 http://deb.debian.org/debian bookworm/main amd64 libjetty9-java all 9.4.50-4+deb12u2 [2981 kB]
Get: 367 http://deb.debian.org/debian bookworm/main amd64 libjsoup-java all 1.15.3-1 [431 kB]
Get: 368 http://deb.debian.org/debian bookworm/main amd64 libjtidy-java all 7+svn20110807-5 [250 kB]
Get: 369 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB]
Get: 370 http://deb.debian.org/debian bookworm/main amd64 libmaven-antrun-plugin-java all 3.1.0-1 [36.9 kB]
Get: 371 http://deb.debian.org/debian bookworm/main amd64 libmaven-common-artifact-filters-java all 3.3.2-1 [48.2 kB]
Get: 372 http://deb.debian.org/debian bookworm/main amd64 libmaven-artifact-transfer-java all 0.13.1-2 [158 kB]
Get: 373 http://deb.debian.org/debian bookworm/main amd64 libplexus-build-api-java all 0.0.7-4 [10.3 kB]
Get: 374 http://deb.debian.org/debian bookworm/main amd64 libmaven-filtering-java all 3.3.0-1 [50.2 kB]
Get: 375 http://deb.debian.org/debian bookworm/main amd64 libmaven-assembly-plugin-java all 3.4.2-1 [242 kB]
Get: 376 http://deb.debian.org/debian bookworm/main amd64 libmaven-clean-plugin-java all 3.2.0-2 [32.2 kB]
Get: 377 http://deb.debian.org/debian bookworm/main amd64 libmaven-shared-incremental-java all 1.1-3 [9524 B]
Get: 378 http://deb.debian.org/debian bookworm/main amd64 libplexus-compiler-java all 2.12.1-1 [99.8 kB]
Get: 379 http://deb.debian.org/debian bookworm/main amd64 libqdox2-java all 2.0.3-1 [296 kB]
Get: 380 http://deb.debian.org/debian bookworm/main amd64 libplexus-languages-java all 1.1.1-2 [47.3 kB]
Get: 381 http://deb.debian.org/debian bookworm/main amd64 libmaven-compiler-plugin-java all 3.10.1-2 [59.0 kB]
Get: 382 http://deb.debian.org/debian bookworm/main amd64 libmaven-dependency-analyzer-java all 1.13.0-1 [30.4 kB]
Get: 383 http://deb.debian.org/debian bookworm/main amd64 libmaven-dependency-tree-java all 3.2.1-1 [34.7 kB]
Get: 384 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-impl-java all 3.2.0-2 [15.2 kB]
Get: 385 http://deb.debian.org/debian bookworm/main amd64 libmaven-dependency-plugin-java all 3.5.0-1 [173 kB]
Get: 386 http://deb.debian.org/debian bookworm/main amd64 libmaven-invoker-java all 3.2.0-1 [28.1 kB]
Get: 387 http://deb.debian.org/debian bookworm/main amd64 libplexus-interactivity-api-java all 1.1-2 [11.0 kB]
Get: 388 http://deb.debian.org/debian bookworm/main amd64 libmaven-javadoc-plugin-java all 3.4.1-2 [454 kB]
Get: 389 http://deb.debian.org/debian bookworm/main amd64 libplexus-container-default1.5-java all 2.1.1-1 [4476 B]
Get: 390 http://deb.debian.org/debian bookworm/main amd64 libplexus-ant-factory-java all 1.0~alpha2.1-4 [11.4 kB]
Get: 391 http://deb.debian.org/debian bookworm/main amd64 libplexus-bsh-factory-java all 1.0~alpha7-5 [8360 B]
Get: 392 http://deb.debian.org/debian bookworm/main amd64 libmaven-plugin-tools-java all 3.7.1-1 [265 kB]
Get: 393 http://deb.debian.org/debian bookworm/main amd64 libmaven-reporting-exec-java all 1.6.0-1 [26.8 kB]
Get: 394 http://deb.debian.org/debian bookworm/main amd64 libmaven-resources-plugin-java all 3.3.0-1 [28.4 kB]
Get: 395 http://deb.debian.org/debian bookworm/main amd64 libmaven-site-plugin-java all 3.12.1-2 [107 kB]
Get: 396 http://deb.debian.org/debian bookworm/main amd64 libmaven-source-plugin-java all 3.2.1-2 [27.6 kB]
Get: 397 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB]
Get: 398 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B]
Get: 399 http://deb.debian.org/debian bookworm/main amd64 libpicard-java all 2.27.5+dfsg-2 [1725 kB]
Get: 400 http://deb.debian.org/debian bookworm/main amd64 libpj-java all 0.0~20150107+dfsg-4 [1377 kB]
Get: 401 http://deb.debian.org/debian bookworm/main amd64 libpkgconf3 amd64 1.8.1-1 [36.1 kB]
Get: 402 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB]
Get: 403 http://deb.debian.org/debian bookworm/main amd64 libprotobuf32 amd64 3.21.12-3 [932 kB]
Get: 404 http://deb.debian.org/debian bookworm/main amd64 libprotobuf-lite32 amd64 3.21.12-3 [261 kB]
Get: 405 http://deb.debian.org/debian bookworm/main amd64 libprotobuf-dev amd64 3.21.12-3 [1283 kB]
Get: 406 http://deb.debian.org/debian bookworm/main amd64 libprotobuf-java all 3.21.12-3 [1257 kB]
Get: 407 http://deb.debian.org/debian bookworm/main amd64 libprotoc32 amd64 3.21.12-3 [829 kB]
Get: 408 http://deb.debian.org/debian bookworm/main amd64 libreflections-java all 0.10.2+dfsg-1 [124 kB]
Get: 409 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB]
Get: 410 http://deb.debian.org/debian bookworm/main amd64 libsurefire-java all 2.22.3-2 [1169 kB]
Get: 411 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB]
Get: 412 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB]
Get: 413 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB]
Get: 414 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB]
Get: 415 http://deb.debian.org/debian bookworm/main amd64 libwagon-file-java all 3.5.3-1 [8388 B]
Get: 416 http://deb.debian.org/debian bookworm/main amd64 libwagon-http-shaded-java all 3.5.3-1 [1341 kB]
Get: 417 http://deb.debian.org/debian bookworm/main amd64 libxml2-utils amd64 2.9.14+dfsg-1.3~deb12u1 [98.9 kB]
Get: 418 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB]
Get: 419 http://deb.debian.org/debian bookworm/main amd64 maven all 3.8.7-1 [18.9 kB]
Get: 420 http://deb.debian.org/debian bookworm/main amd64 maven-repo-helper all 1.11 [142 kB]
Get: 421 http://deb.debian.org/debian bookworm/main amd64 maven-debian-helper all 2.6.3 [108 kB]
Get: 422 http://deb.debian.org/debian bookworm/main amd64 pkgconf-bin amd64 1.8.1-1 [29.5 kB]
Get: 423 http://deb.debian.org/debian bookworm/main amd64 pkgconf amd64 1.8.1-1 [25.9 kB]
Get: 424 http://deb.debian.org/debian bookworm/main amd64 pkg-config amd64 1.8.1-1 [13.7 kB]
Get: 425 http://deb.debian.org/debian bookworm/main amd64 protobuf-compiler amd64 3.21.12-3 [83.9 kB]
Get: 426 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB]
Get: 427 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB]
Get: 428 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB]
Get: 429 http://deb.debian.org/debian bookworm/main amd64 r-cran-rjava amd64 1.0-6-1+b1 [917 kB]
Get: 430 http://deb.debian.org/debian bookworm/main amd64 testng all 6.9.12-4 [795 kB]
Fetched 381 MB in 4s (103 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libpython3.11-minimal:amd64.
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Setting up libpython3.11-minimal:amd64 (3.11.2-6) ...
Setting up libexpat1:amd64 (2.5.0-1) ...
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Selecting previously unselected package python3-minimal.
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Unpacking python3-minimal (3.11.2-1+b1) ...
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Unpacking readline-common (8.2-1.3) ...
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Unpacking libreadline8:amd64 (8.2-1.3) ...
Selecting previously unselected package libpython3.11-stdlib:amd64.
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Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ...
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Unpacking python3.11 (3.11.2-6) ...
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Setting up python3-minimal (3.11.2-1+b1) ...
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Unpacking python3 (3.11.2-1+b1) ...
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Unpacking procps (2:4.0.2-3) ...
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Unpacking sensible-utils (0.0.17+nmu1) ...
Selecting previously unselected package openssl.
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Unpacking openssl (3.0.11-1~deb12u2) ...
Selecting previously unselected package ca-certificates.
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Unpacking ca-certificates (20230311) ...
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Unpacking libmagic-mgc (1:5.44-3) ...
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Unpacking gettext-base (0.21-12) ...
Selecting previously unselected package libuchardet0:amd64.
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Unpacking bsdextrautils (2.38.1-5+b1) ...
Selecting previously unselected package libpipeline1:amd64.
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Unpacking libpipeline1:amd64 (1.5.7-1) ...
Selecting previously unselected package man-db.
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Setting up libcommons-parent-java (56-1) ...
Setting up libavahi-common3:amd64 (0.8-10) ...
Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ...
Setting up libcommons-logging-java (1.2-3) ...
Setting up libnet-http-perl (6.22-1) ...
Setting up libsisu-inject-java (0.3.4-2) ...
Setting up libnss3:amd64 (2:3.87.1-1) ...
Setting up libxcb-shm0:amd64 (1.15-1) ...
Setting up libdevel-callchecker-perl:amd64 (0.008-2) ...
Setting up libcommons-lang-java (2.6-10) ...
Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ...
Setting up libplexus-cipher-java (2.0-1) ...
Setting up pkgconf:amd64 (1.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libprotobuf-dev:amd64 (3.21.12-3) ...
Setting up libxcb-present0:amd64 (1.15-1) ...
Setting up dh-autoreconf (20) ...
Setting up patchutils (0.4.2-1) ...
Setting up libcommons-jexl2-java (2.1.1-6) ...
Setting up libthai0:amd64 (0.1.29-1) ...
Setting up ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
140 added, 0 removed; done.
Setting up libsisu-plexus-java (0.3.4-3) ...
Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ...
Setting up libxcb-sync1:amd64 (1.15-1) ...
Setting up libxalan2-java (2.7.2-4) ...
Setting up testng (6.9.12-4) ...
Setting up shared-mime-info (2.2-1) ...
Setting up libcommons-collections4-java (4.2-1) ...
Setting up pkg-config:amd64 (1.8.1-1) ...
Setting up ucf (3.0043+nmu1) ...
Setting up libcommons-lang3-java (3.12.0-2) ...
Setting up libxcb-dri2-0:amd64 (1.15-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up libwww-robotrules-perl (6.02-1) ...
Setting up libdrm2:amd64 (2.4.114-1+b1) ...
Setting up dwz (0.15-1) ...
Setting up libmaven-common-artifact-filters-java (3.3.2-1) ...
Setting up groff-base (1.22.4-10) ...
Setting up libxcb-randr0:amd64 (1.15-1) ...
Setting up libhtml-parser-perl:amd64 (3.81-1) ...
Setting up libllvm15:amd64 (1:15.0.6-4+b1) ...
Setting up gpgconf (2.2.40-1.1) ...
Setting up libcommons-beanutils-java (1.9.4-1) ...
Setting up libcurl4:amd64 (7.88.1-10+deb12u4) ...
Setting up libplexus-sec-dispatcher-java (2.0-3) ...
Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ...
Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ...
Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ...
Setting up libsnappy-java (1.1.8.3-1) ...
Setting up libfontconfig1:amd64 (2.14.1-4) ...
Setting up ca-certificates-java (20230710~deb12u1) ...
No JRE found. Skipping Java certificates setup.
Setting up libcommons-configuration-java (1.10-6) ...
Setting up libwagon-file-java (3.5.3-1) ...
Setting up libxml2-utils (2.9.14+dfsg-1.3~deb12u1) ...
Setting up libcommons-codec-java (1.15-1) ...
Setting up libxcomposite1:amd64 (1:0.4.5-1) ...
Setting up libsm6:amd64 (2:1.2.3-1) ...
Setting up libreflections-java (0.10.2+dfsg-1) ...
Setting up libavahi-client3:amd64 (0.8-10) ...
Setting up libio-socket-ssl-perl (2.081-2) ...
Setting up gpg (2.2.40-1.1) ...
Setting up gnupg-utils (2.2.40-1.1) ...
Setting up libhttp-message-perl (6.44-1) ...
Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ...
Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6~deb12u1) ...
Setting up libxcb-dri3-0:amd64 (1.15-1) ...
Setting up libpaper1:amd64 (1.1.29) ...

Creating config file /etc/papersize with new version
Setting up gtk-update-icon-cache (3.24.38-2~deb12u1) ...
Setting up libx11-xcb1:amd64 (2:1.8.4-2+deb12u2) ...
Setting up libhttp-negotiate-perl (6.01-2) ...
Setting up velocity (1.7-6) ...
Setting up fontconfig (2.14.1-4) ...
Regenerating fonts cache... done.
Setting up libngs-jni:amd64 (3.0.3+dfsg-6~deb12u1) ...
Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ...
Setting up libxdamage1:amd64 (1:1.1.6-1) ...
Setting up gpg-agent (2.2.40-1.1) ...
Setting up libxrender1:amd64 (1:0.9.10-1.1) ...
Setting up libcommons-compress-java (1.22-1) ...
Setting up libhttp-cookies-perl (6.10-1) ...
Setting up libcommons-io-java (2.11.0-2) ...
Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ...
Setting up libcommons-digester-java (1.8.1-5) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhtml-tree-perl (5.07-3) ...
Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ...
Setting up libdistlib-java (1.0-4) ...
Setting up libparams-classify-perl:amd64 (0.015-2+b1) ...
Setting up gpgsm (2.2.40-1.1) ...
Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ...
Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ...
Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ...
Setting up libxext6:amd64 (2:1.3.4-1+b1) ...
Setting up libxmlgraphics-commons-java (2.8-2) ...
Setting up libpaper-utils (1.1.29) ...
Setting up man-db (2.11.2-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:amd64 (1.16.0-7) ...
Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ...
Setting up dirmngr (2.2.40-1.1) ...
Setting up libmaven-filtering-java (3.3.0-1) ...
Setting up libmaven-resolver-java (1.6.3-1) ...
Setting up adwaita-icon-theme (43-1) ...
update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode
Setting up libmodule-runtime-perl (0.016-2) ...
Setting up libxfixes3:amd64 (1:6.0.0-2) ...
Setting up libxinerama1:amd64 (2:1.1.4-3) ...
Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ...
Setting up libxt6:amd64 (1:1.2.1-1.1) ...
Setting up gpg-wks-server (2.2.40-1.1) ...
Setting up libcups2:amd64 (2.4.2-3+deb12u5) ...
Setting up libhttpclient-java (4.5.14-1) ...
Setting up libmaven-dependency-tree-java (3.2.1-1) ...
Setting up liblightcouch-java (0.2.0-1) ...
Setting up libmaven-shared-utils-java (3.3.4-1) ...
Setting up libxss1:amd64 (1:1.2.3-1) ...
Setting up libngs-java:amd64 (3.0.3+dfsg-6~deb12u1) ...
Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ...
Setting up libmaven-resources-plugin-java (3.3.0-1) ...
Setting up libhtsjdk-java (3.0.4+dfsg-2) ...
Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ...
Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ...
Setting up python3.11 (3.11.2-6) ...
Setting up libxft2:amd64 (2.3.6-1) ...
Setting up libplexus-io-java (3.3.1-2) ...
Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ...
Setting up libxi6:amd64 (2:1.8-1+b1) ...
Setting up gpg-wks-client (2.2.40-1.1) ...
Setting up libglx0:amd64 (1.6.0-1) ...
Setting up libcommons-validator-java (1:1.7-1) ...
Setting up libimport-into-perl (1.002005-2) ...
Setting up libxtst6:amd64 (2:1.2.3-1.1) ...
Setting up libbatik-java (1.16+dfsg-1+deb12u1) ...
Setting up libmoo-perl (2.005005-1) ...
Setting up liblog4j2-java (2.19.0-2) ...
Setting up libtk8.6:amd64 (8.6.13-2) ...
Setting up libxcursor1:amd64 (1:1.2.1-1) ...
Setting up libmaven-invoker-java (3.2.0-1) ...
Setting up debhelper (13.11.4) ...
Setting up python3 (3.11.2-1+b1) ...
Setting up libgl1:amd64 (1.6.0-1) ...
Setting up r-base-core (4.2.2.20221110-2) ...

Creating config file /etc/R/Renviron with new version
Setting up libmaven-clean-plugin-java (3.2.0-2) ...
Setting up openjdk-17-jre-headless:amd64 (17.0.9+9-1~deb12u1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode
Setting up gnupg (2.2.40-1.1) ...
Setting up libplexus-archiver-java (4.6.1-1) ...
Setting up libbarclay-java (4.1.0+dfsg-1) ...
Setting up libfop-java (1:2.8-2) ...
Setting up libgkl-java (0.8.10+dfsg-3) ...
Setting up libgtk2.0-0:amd64 (2.24.33-2) ...
Setting up libmaven-archiver-java (3.6.0-1) ...
Setting up libpicard-java (2.27.5+dfsg-2) ...
Setting up liblwp-protocol-https-perl (6.10-1) ...
Setting up liberror-prone-java (2.18.0-1) ...
Setting up libwww-perl (6.68-1) ...
Setting up devscripts (2.23.4+deb12u1) ...
Setting up libguava-java (31.1-1) ...
Setting up javahelper (0.78) ...
Setting up libplexus-container-default-java (2.1.1-1) ...
Setting up libguice-java (4.2.3-2) ...
Setting up libplexus-i18n-java (1.0-beta-10-6) ...
Setting up libplexus-container-default1.5-java (2.1.1-1) ...
Setting up libplexus-interactivity-api-java (1.1-2) ...
Setting up libplexus-velocity-java (1.2-3.1) ...
Setting up libmaven3-core-java (3.8.7-1) ...
Setting up libmaven-shared-incremental-java (1.1-3) ...
Setting up libmaven-shared-io-java (3.0.0-4) ...
Setting up libplexus-bsh-factory-java (1.0~alpha7-5) ...
Setting up libmaven-dependency-analyzer-java (1.13.0-1) ...
Setting up libplexus-compiler-java (2.12.1-1) ...
Setting up libmaven-compiler-plugin-java (3.10.1-2) ...
Setting up libmaven-artifact-transfer-java (0.13.1-2) ...
Setting up libmaven-file-management-java (3.0.0-1) ...
Setting up libmaven-source-plugin-java (3.2.1-2) ...
Setting up libbyte-buddy-java (1.12.21-1) ...
Setting up libbuild-helper-maven-plugin-java (3.3.0-1) ...
Setting up libeasymock-java (5.1.0-1) ...
Setting up libmaven-jar-plugin-java (3.3.0-2) ...
Setting up libmaven-assembly-plugin-java (3.4.2-1) ...
Setting up libcommons-text-java (1.10.0-1) ...
Setting up libdoxia-core-java (1.12.0-1) ...
Setting up libdoxia-java (1.12.0-1) ...
Setting up libmaven-reporting-api-java (3.1.1-1) ...
Setting up libmaven-reporting-exec-java (1.6.0-1) ...
Processing triggers for libc-bin (2.36-9+deb12u3) ...
Processing triggers for ca-certificates-java (20230710~deb12u1) ...
Adding debian:ACCVRAIZ1.pem
Adding debian:AC_RAIZ_FNMT-RCM.pem
Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem
Adding debian:ANF_Secure_Server_Root_CA.pem
Adding debian:Actalis_Authentication_Root_CA.pem
Adding debian:AffirmTrust_Commercial.pem
Adding debian:AffirmTrust_Networking.pem
Adding debian:AffirmTrust_Premium.pem
Adding debian:AffirmTrust_Premium_ECC.pem
Adding debian:Amazon_Root_CA_1.pem
Adding debian:Amazon_Root_CA_2.pem
Adding debian:Amazon_Root_CA_3.pem
Adding debian:Amazon_Root_CA_4.pem
Adding debian:Atos_TrustedRoot_2011.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem
Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem
Adding debian:Baltimore_CyberTrust_Root.pem
Adding debian:Buypass_Class_2_Root_CA.pem
Adding debian:Buypass_Class_3_Root_CA.pem
Adding debian:CA_Disig_Root_R2.pem
Adding debian:CFCA_EV_ROOT.pem
Adding debian:COMODO_Certification_Authority.pem
Adding debian:COMODO_ECC_Certification_Authority.pem
Adding debian:COMODO_RSA_Certification_Authority.pem
Adding debian:Certainly_Root_E1.pem
Adding debian:Certainly_Root_R1.pem
Adding debian:Certigna.pem
Adding debian:Certigna_Root_CA.pem
Adding debian:Certum_EC-384_CA.pem
Adding debian:Certum_Trusted_Network_CA.pem
Adding debian:Certum_Trusted_Network_CA_2.pem
Adding debian:Certum_Trusted_Root_CA.pem
Adding debian:Comodo_AAA_Services_root.pem
Adding debian:D-TRUST_BR_Root_CA_1_2020.pem
Adding debian:D-TRUST_EV_Root_CA_1_2020.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem
Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem
Adding debian:DigiCert_Assured_ID_Root_CA.pem
Adding debian:DigiCert_Assured_ID_Root_G2.pem
Adding debian:DigiCert_Assured_ID_Root_G3.pem
Adding debian:DigiCert_Global_Root_CA.pem
Adding debian:DigiCert_Global_Root_G2.pem
Adding debian:DigiCert_Global_Root_G3.pem
Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem
Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem
Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem
Adding debian:DigiCert_Trusted_Root_G4.pem
Adding debian:E-Tugra_Certification_Authority.pem
Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem
Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem
Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem
Adding debian:Entrust_Root_Certification_Authority.pem
Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem
Adding debian:Entrust_Root_Certification_Authority_-_G2.pem
Adding debian:Entrust_Root_Certification_Authority_-_G4.pem
Adding debian:GDCA_TrustAUTH_R5_ROOT.pem
Adding debian:GLOBALTRUST_2020.pem
Adding debian:GTS_Root_R1.pem
Adding debian:GTS_Root_R2.pem
Adding debian:GTS_Root_R3.pem
Adding debian:GTS_Root_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem
Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem
Adding debian:GlobalSign_Root_CA.pem
Adding debian:GlobalSign_Root_CA_-_R3.pem
Adding debian:GlobalSign_Root_CA_-_R6.pem
Adding debian:GlobalSign_Root_E46.pem
Adding debian:GlobalSign_Root_R46.pem
Adding debian:Go_Daddy_Class_2_CA.pem
Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem
Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem
Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem
Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem
Adding debian:HiPKI_Root_CA_-_G1.pem
Adding debian:Hongkong_Post_Root_CA_1.pem
Adding debian:Hongkong_Post_Root_CA_3.pem
Adding debian:ISRG_Root_X1.pem
Adding debian:ISRG_Root_X2.pem
Adding debian:IdenTrust_Commercial_Root_CA_1.pem
Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem
Adding debian:Izenpe.com.pem
Adding debian:Microsec_e-Szigno_Root_CA_2009.pem
Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem
Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem
Adding debian:NAVER_Global_Root_Certification_Authority.pem
Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem
Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem
Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem
Adding debian:QuoVadis_Root_CA_1_G3.pem
Adding debian:QuoVadis_Root_CA_2.pem
Adding debian:QuoVadis_Root_CA_2_G3.pem
Adding debian:QuoVadis_Root_CA_3.pem
Adding debian:QuoVadis_Root_CA_3_G3.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem
Adding debian:SSL.com_Root_Certification_Authority_ECC.pem
Adding debian:SSL.com_Root_Certification_Authority_RSA.pem
Adding debian:SZAFIR_ROOT_CA2.pem
Adding debian:SecureSign_RootCA11.pem
Adding debian:SecureTrust_CA.pem
Adding debian:Secure_Global_CA.pem
Adding debian:Security_Communication_ECC_RootCA1.pem
Adding debian:Security_Communication_RootCA2.pem
Adding debian:Security_Communication_RootCA3.pem
Adding debian:Security_Communication_Root_CA.pem
Adding debian:Starfield_Class_2_CA.pem
Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem
Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem
Adding debian:SwissSign_Gold_CA_-_G2.pem
Adding debian:SwissSign_Silver_CA_-_G2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_2.pem
Adding debian:T-TeleSec_GlobalRoot_Class_3.pem
Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem
Adding debian:TWCA_Global_Root_CA.pem
Adding debian:TWCA_Root_Certification_Authority.pem
Adding debian:TeliaSonera_Root_CA_v1.pem
Adding debian:Telia_Root_CA_v2.pem
Adding debian:TrustCor_ECA-1.pem
Adding debian:TrustCor_RootCert_CA-1.pem
Adding debian:TrustCor_RootCert_CA-2.pem
Adding debian:Trustwave_Global_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem
Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem
Adding debian:TunTrust_Root_CA.pem
Adding debian:UCA_Extended_Validation_Root.pem
Adding debian:UCA_Global_G2_Root.pem
Adding debian:USERTrust_ECC_Certification_Authority.pem
Adding debian:USERTrust_RSA_Certification_Authority.pem
Adding debian:XRamp_Global_CA_Root.pem
Adding debian:certSIGN_ROOT_CA.pem
Adding debian:certSIGN_Root_CA_G2.pem
Adding debian:e-Szigno_Root_CA_2017.pem
Adding debian:ePKI_Root_Certification_Authority.pem
Adding debian:emSign_ECC_Root_CA_-_C3.pem
Adding debian:emSign_ECC_Root_CA_-_G3.pem
Adding debian:emSign_Root_CA_-_C1.pem
Adding debian:emSign_Root_CA_-_G1.pem
Adding debian:vTrus_ECC_Root_CA.pem
Adding debian:vTrus_Root_CA.pem
done.
Setting up maven-repo-helper (1.11) ...
Setting up maven (3.8.7-1) ...
update-alternatives: using /usr/share/maven/bin/mvn to provide /usr/bin/mvn (mvn) in auto mode
Setting up openjdk-17-jdk-headless:amd64 (17.0.9+9-1~deb12u1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode
Setting up ant (1.10.13-1) ...
Setting up junit4 (4.13.2-3) ...
Setting up default-jre-headless (2:1.17-74) ...
Setting up ant-contrib (1.0~b3+svn177-12) ...
Setting up openjdk-17-jre:amd64 (17.0.9+9-1~deb12u1) ...
Setting up libconcurrent-java (1.3.4-6) ...
Setting up default-jre (2:1.17-74) ...
Setting up openjdk-17-jdk:amd64 (17.0.9+9-1~deb12u1) ...
update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode
Setting up libmaven-antrun-plugin-java (3.1.0-1) ...
Setting up libplexus-ant-factory-java (1.0~alpha2.1-4) ...
Setting up default-jdk-headless (2:1.17-74) ...
Setting up libjsap-java (2.1-5) ...
Setting up r-cran-rjava (1.0-6-1+b1) ...
Setting up libcolt-free-java (1.2.0+dfsg-7) ...
Setting up libdsiutils-java (2.7.2+dfsg-1) ...
Setting up junit5 (5.9.2-1) ...
Setting up default-jdk (2:1.17-74) ...
Setting up libicb-utils-java (2.0.1+git20161002.afee1d9-5) ...
Processing triggers for sgml-base (1.31) ...
Setting up libvelocity-tools-java (2.0-8) ...
Setting up libdoxia-sitetools-java (1.11.1-1) ...
Setting up libmaven-site-plugin-java (3.12.1-2) ...
Setting up libmaven-javadoc-plugin-java (3.4.1-2) ...
Setting up libmaven-reporting-impl-java (3.2.0-2) ...
Setting up libmaven-dependency-plugin-java (3.5.0-1) ...
Setting up libmaven-plugin-tools-java (3.7.1-1) ...
Setting up libsurefire-java (2.22.3-2) ...
Setting up maven-debian-helper (2.6.3) ...
Processing triggers for ca-certificates (20230311) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
Processing triggers for ca-certificates-java (20230710~deb12u1) ...
done.
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
I: Building the package
I: user script /srv/workspace/pbuilder/2185384/tmp/hooks/A99_set_merged_usr starting
Not re-configuring usrmerge for bookworm
I: user script /srv/workspace/pbuilder/2185384/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+dfsg2-9_source.changes
dpkg-buildpackage: info: source package libgoby-java
dpkg-buildpackage: info: source version 3.3.1+dfsg2-9
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Pierre Gruet <pgt@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean --with javahelper
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2'
dh_auto_clean
	bash -c "for dir in \$(find . -name target -type d); do if [ -f \$(echo \$dir | sed -e s/target\$/pom.xml/) ]; then rm -Rf \$dir; fi done"
	mh_unpatchpoms -plibgoby-io-java
rm -f goby-distribution/test-data
rm -rf test-results/
make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2'
   jh_clean
   dh_clean
 debian/rules binary
dh binary --with javahelper
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
	mh_patchpoms -plibgoby-io-java --debian-build --keep-pom-version --maven-repo=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo
   jh_linkjars
   dh_auto_build
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode package -DskipTests -Dnotimestamp=true -Dlocale=en_US
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
[WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Goby Framework                                                     [pom]
[INFO] Goby I/O                                                           [jar]
[INFO] Goby Full Distribution                                             [jar]
[INFO] 
[INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
[INFO] Building Goby Framework 3.3.1                                      [1/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
[INFO] Building Goby I/O 3.3.1                                            [2/3]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.0
[WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3
[WARNING] The artifact org.apache.maven.plugins:maven-jar-plugin:jar:2.4 has been relocated to org.apache.maven.plugins:maven-jar-plugin:jar:3.3.0
[INFO] 
[INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-classes) @ goby-io ---
[INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO]     [mkdir] Created dir: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-io ---
[INFO] Copying 2 resources
[INFO] Copying 1 resource
[INFO] Copying 1 resource
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-io ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 260 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (default) @ goby-io ---
[WARNING] Parameter tasks is deprecated, use target instead
[INFO] Executing tasks
[INFO]      [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2
[INFO]      [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ goby-io ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-io ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-io ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ goby-io ---
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1.jar
[INFO] 
[INFO] >>> maven-source-plugin:3.2.1:jar (attach-sources) > generate-sources @ goby-io >>>
[INFO] 
[INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-classes) @ goby-io ---
[INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] <<< maven-source-plugin:3.2.1:jar (attach-sources) < generate-sources @ goby-io <<<
[INFO] 
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar (attach-sources) @ goby-io ---
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.4.1:jar (attach-javadocs) @ goby-io ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] Loading source files for package samples...
[WARNING] Loading source files for package org.campagnelab.goby.xml...
[WARNING] Loading source files for package org.campagnelab.goby.util.pool...
[WARNING] Loading source files for package org.campagnelab.goby.util.motifs...
[WARNING] Loading source files for package org.campagnelab.goby.util.dynoptions...
[WARNING] Loading source files for package org.campagnelab.goby.util.commits...
[WARNING] Loading source files for package org.campagnelab.goby.util.barcode...
[WARNING] Loading source files for package org.campagnelab.goby.util...
[WARNING] Loading source files for package org.campagnelab.goby.stats...
[WARNING] Loading source files for package org.campagnelab.goby.reads...
[WARNING] Loading source files for package org.campagnelab.goby.readers.vcf...
[WARNING] Loading source files for package org.campagnelab.goby.readers.sam...
[WARNING] Loading source files for package org.campagnelab.goby.readers...
[WARNING] Loading source files for package org.campagnelab.goby.predictions...
[WARNING] Loading source files for package org.campagnelab.goby.parsers...
[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.dsv...
[WARNING] Loading source files for package org.campagnelab.goby.modes.core...
[WARNING] Loading source files for package org.campagnelab.goby.methylation...
[WARNING] Loading source files for package org.campagnelab.goby.exception...
[WARNING] Loading source files for package org.campagnelab.goby.counts.compound...
[WARNING] Loading source files for package org.campagnelab.goby.counts...
[WARNING] Loading source files for package org.campagnelab.goby.config...
[WARNING] Loading source files for package org.campagnelab.goby.compression...
[WARNING] Loading source files for package org.campagnelab.goby.cli...
[WARNING] Loading source files for package org.campagnelab.goby.baseinfo...
[WARNING] Loading source files for package org.campagnelab.goby.alignments...
[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.alignments.htsjdk...
[WARNING] Loading source files for package org.campagnelab.goby.alignments.filters...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.indels...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.dsv...
[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.data...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.compression...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm.dmr...
[WARNING] Loading source files for package org.campagnelab.goby.algorithmic.algorithm...
[WARNING] Loading source files for package org.campagnelab.goby...
[WARNING] Loading source files for package org.campagnelab.goby.R...
[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/xml/MethylStats.java:21: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlRootElement;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/xml/MethylStats.java:31: error: cannot find symbol
[WARNING] @XmlRootElement
[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/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/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/stats/FisherExactRCalculator.java:68: error: cannot find symbol
[WARNING] Rengine rEngine;
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class FisherExactRCalculator
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/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/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/modes/PercentMismatchesQualityFilter.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/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/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/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] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/RunParallelMode.java:31: error: package org.apache.commons.exec does not exist
[WARNING] import org.apache.commons.exec.DefaultExecutor;
[WARNING] ^
[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/MethylStatsMode.java:34: 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/MethylStatsMode.java:35: 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/MethylStatsMode.java:36: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.Marshaller;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/MethylStatsMode.java:696: error: cannot find symbol
[WARNING] private void writeXml(PrintWriter output, String[] samples, MethylStats[] methylStats) throws JAXBException {
[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/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/CompactAlignmentToAnnotationCountsMode.java:39: 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/modes/CompactAlignmentToAnnotationCountsMode.java:40: 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/modes/CompactAlignmentToAnnotationCountsMode.java:41: 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/CompactAlignmentToAnnotationCountsMode.java:53: 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/CompactAlignmentToAnnotationCountsMode.java:54: 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/CompactAlignmentToAnnotationCountsMode.java:55: error: package javax.xml.bind does not exist
[WARNING] import javax.xml.bind.Marshaller;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:106: error: cannot find symbol
[WARNING] private ParallelTeam team;
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[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/CompactAlignmentToAnnotationCountsMode.java:325: error: cannot find symbol
[WARNING] protected synchronized ParallelTeam getParallelTeam() {
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[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] /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] /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] /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 XmlRootElement
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.java:441: error: cannot find symbol
[WARNING] private void writeInfoOutput() throws JAXBException, IOException {
[WARNING] ^
[WARNING] symbol:   class JAXBException
[WARNING] location: class CompactAlignmentToAnnotationCountsMode
[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/algorithmic/data/xml/AnnotationLength.java:22: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessorType;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[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/SampleTotalCount.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/algorithmic/data/xml/SampleTotalCount.java:22: error: package javax.xml.bind.annotation does not exist
[WARNING] import javax.xml.bind.annotation.XmlAccessorType;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[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/modes/CompactAlignmentToAnnotationCountsMode.java:283: error: cannot find symbol
[WARNING] class BasenameParallelRegion extends ParallelRegion {
[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/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/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/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/methylation/MethylSimilarityScan.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/cli/PlantIndels.java:22: error: package org.apache.commons.cli does not exist
[WARNING] import org.apache.commons.cli.*;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/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/DoInParallel.java:21: 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/cli/DoInParallel.java:33: error: cannot find symbol
[WARNING] private ParallelTeam team;
[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/DoInParallel.java:47: error: cannot find symbol
[WARNING] protected synchronized ParallelTeam getParallelTeam() {
[WARNING] ^
[WARNING] symbol:   class ParallelTeam
[WARNING] location: class DoInParallel
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:23: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.IntegerForLoop;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/BasenameParallelRegion.java:24: error: package edu.rit.pj does not exist
[WARNING] import edu.rit.pj.ParallelRegion;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/cli/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/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/RLoggerMainLoopCallback.java:23: 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/R/RLoggerMainLoopCallback.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/R/RLoggerMainLoopCallback.java:29: error: cannot find symbol
[WARNING] class RLoggerMainLoopCallback implements RMainLoopCallbacks {
[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/RLoggerMainLoopCallback.java:42: error: cannot find symbol
[WARNING] public void rWriteConsole(final Rengine rengine, final String text, final int type) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:57: error: cannot find symbol
[WARNING] public void rBusy(final Rengine rengine, final int which) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:77: error: cannot find symbol
[WARNING] public String rReadConsole(final Rengine rengine, final String prompt, final int addToHistory) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:88: error: cannot find symbol
[WARNING] public void rShowMessage(final Rengine rengine, final String message) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:99: error: cannot find symbol
[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:108: error: cannot find symbol
[WARNING] public void rFlushConsole(final Rengine rengine) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:118: error: cannot find symbol
[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RLoggerMainLoopCallback.java:127: error: cannot find symbol
[WARNING] public void rLoadHistory(final Rengine re, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RLoggerMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/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/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/R/RConsoleMainLoopCallback.java:27: error: cannot find symbol
[WARNING] class RConsoleMainLoopCallback implements RMainLoopCallbacks {
[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] ^
[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] 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] 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 Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:92: error: cannot find symbol
[WARNING] public String rChooseFile(final Rengine rengine, final int newFile) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:101: error: cannot find symbol
[WARNING] public void rFlushConsole(final Rengine rengine) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:111: error: cannot find symbol
[WARNING] public void rSaveHistory(final Rengine rengine, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/RConsoleMainLoopCallback.java:120: error: cannot find symbol
[WARNING] public void rLoadHistory(final Rengine re, final String filename) {
[WARNING] ^
[WARNING] symbol:   class Rengine
[WARNING] location: class RConsoleMainLoopCallback
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/R/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/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/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] ^
[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/algorithmic/data/xml/AnnotationLength.java:29: error: cannot find symbol
[WARNING] @XmlAccessorType(XmlAccessType.FIELD)
[WARNING] ^
[WARNING] symbol: variable XmlAccessType
[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:35: error: cannot find symbol
[WARNING] @XmlElement(name = "al")
[WARNING] ^
[WARNING] symbol:   class XmlElement
[WARNING] location: class InfoOutput
[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:36: error: cannot find symbol
[WARNING] @XmlElementWrapper(name = "annotation-lengths")
[WARNING] ^
[WARNING] symbol:   class XmlElementWrapper
[WARNING] location: class InfoOutput
[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: variable XmlAccessType
[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:39: error: cannot find symbol
[WARNING] @XmlElement(name = "tc")
[WARNING] ^
[WARNING] symbol:   class XmlElement
[WARNING] location: class InfoOutput
[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:40: error: cannot find symbol
[WARNING] @XmlElementWrapper(name = "total-counts")
[WARNING] ^
[WARNING] symbol:   class XmlElementWrapper
[WARNING] location: class InfoOutput
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
[WARNING] Building tree for all the packages and classes...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.TransferIds.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractCommandLineMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AbstractGobyMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByPeakDistanceMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../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-io/../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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollection.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentCollectionOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntry.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentEntryOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeader.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentHeaderOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndex.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentIndexOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHits.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AlignmentTooManyHitsOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocation.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.AmbiguousLocationOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfo.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierInfoOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMapping.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.IdentifierMappingOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfo.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.ReadOriginInfoOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntry.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.RelatedAlignmentEntryOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariation.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/Alignments.SequenceVariationOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/AnnotationsToCountsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformation.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollection.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationCollectionOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.BaseInformationOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfo.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.CountInfoOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequency.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.NumberWithFrequencyOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfo.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SampleInfoOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutput.Builder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/BaseInformationRecords.SomaticOutputOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BisulfiteConversionMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../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] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../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-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/By5BinningStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/CodecHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<'
[WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors).
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToCountsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixer.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/CountFixerNoThresholdingEffect.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountIndexBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/CountRawSampleIdsCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsAggregatorI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsArchiveReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToBedGraphMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToUnionPeaksAnnotationMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CountsArchiveToWiggleMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsArchiveWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsReaderI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriterHelperI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountsWriterI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/counts/CountWriterHelper2.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/CovariateInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CovariateStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/CoverageAnalysis.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/CoverageMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/CumulativeArrayKeeperFast.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DataProvider.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DefaultAlignmentProcessorFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/DefaultAlignmentReaderFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeltaStatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DeNovoDMRfinder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/DiffAlignmentMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionAnalysis.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionCalculator.ElementType.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DifferentialExpressionResults.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/methylation/DifferentiallyMethylatedRegion.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiploidFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/DiscoverSequenceVariantsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.PositionBaseInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/DiscoverVariantPositionData.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/DisplaySequenceVariationsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterBitSet.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/DistinctIntValueCounterInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/cli/DoInParallel.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/reads/DualRandomAccessSequenceCache.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/modes/DummyFormatConfigurator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyGenomeAlignmentTargetMapper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/stats/DummyObservationWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/DummyProcessorUnsorted.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/predictions/DummyTrueGenotypeHelper.html...
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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.NumberWithFrequency.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.NumberWithFrequencyOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.CountInfo.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.CountInfoOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.SampleInfo.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.SampleInfoOrBuilder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/dl/varanalysis/protobuf/class-use/BaseInformationRecords.BaseInformation.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.BaseInformationOrBuilder.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.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/package-use.html...
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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/package-use.html...
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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/perms/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/apidocs/org/campagnelab/goby/alignments/processors/package-use.html...
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[WARNING] Building index for all classes...
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[WARNING] 100 warnings
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/goby-io-3.3.1-javadoc.jar
[INFO] 
[INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
[INFO] Building Goby Full Distribution 3.3.1                              [3/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-distribution ---
[INFO] Copying 3 resources
[INFO] Copying 72 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-distribution ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 525 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/classes
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ goby-distribution ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-distribution ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 120 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/test-classes
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution ---
[INFO] Tests are skipped.
[INFO] 
[INFO] --- maven-jar-plugin:3.3.0:jar (default-jar) @ goby-distribution ---
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1.jar
[INFO] 
[INFO] >>> maven-source-plugin:3.2.1:jar (attach-sources) > generate-sources @ goby-distribution >>>
[INFO] 
[INFO] <<< maven-source-plugin:3.2.1:jar (attach-sources) < generate-sources @ goby-distribution <<<
[INFO] 
[INFO] 
[INFO] --- maven-source-plugin:3.2.1:jar (attach-sources) @ goby-distribution ---
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1-sources.jar
[INFO] 
[INFO] --- maven-javadoc-plugin:3.4.1:jar (attach-javadocs) @ goby-distribution ---
[INFO] Adding the --ignore-source-errors option
[INFO] No previous run data found, generating javadoc.
[WARNING] Javadoc Warnings
[WARNING] Loading source files for package samples...
[WARNING] Loading source files for package org.campagnelab.goby.xml...
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[WARNING] Constructing Javadoc information...
[WARNING] Building index for all the packages and classes...
[WARNING] Standard Doclet version 17.0.9+9-Debian-1deb12u1
[WARNING] Building tree for all the packages and classes...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AbstractAlignmentEntryFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractAlignmentReader.html...
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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractAlignmentToCompactMode.TransferIds.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractCommandLineMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AbstractConcatAlignmentReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AbstractGobyMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/AbstractMethylationAdapter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AbstractOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/AddTrueGenotypeHelperI.WillKeepI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByPeakDistanceMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AggregatePeaksByRPKMDifferenceMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AlignedCountNormalization.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/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] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignedSequence.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentCollectionHandler.CombinedLists.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/AlignmentHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentPositionComparator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/AlignmentProcessorInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/AlignmentQualityFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReader.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderFactoryBase.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentReaderImpl.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentSliceHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentStats.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToPileupMode.OutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AlignmentToTextMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentToTextWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/AlignmentWriterImpl.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/AlleleFrequencyOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Annotation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AnnotationAveragingWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationCountIterateAlignments.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/AnnotationLength.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationPenaltyMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/AnnotationRPKM.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/AnnotationsToCountsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/AnnotationWeightCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/AnyTransitionCountsIterator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATGCCorrectionWeight.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/AtLeastAQuarterFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ATProportionWeight.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/AverageFisherRCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BarcodeDecoderMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcher.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/BarcodeMatcherResult.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/BasenameUtils.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/BaseProportionWeight.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BaseStatsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/BaseToStringHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BenjaminiHochbergAdjustment.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreAmbiguityAlignmentFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/BestScoreOnlyAlignmentFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/BetweenGroupSequenceVariationOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BinningStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BisulfiteConversionMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BonferroniAdjustment.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingAlignmentWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/BufferedSortingSamBamWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/BuggyDeltaStatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/BuildSequenceCacheMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/BullardUpperQuartileNormalization.html...
[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] /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/algorithmic/algorithm/dmr/By5BinningStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/BZip2ChunkCodec.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CachingCountsArchiveReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ChiSquareTestAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/ChiSquareTestCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ChromosomeMapper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodec.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ChunkCodecHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/CodecHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ColorSpaceConverter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnField.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnFields.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnMetaInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/Columns.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/ColumnType.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/CommitPropertiesStatAccumulator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/CommitPropertyHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/CommonIndelArtifactFilter.java:17: warning: invalid input: '<'
[WARNING] * larger than expected (P<0.05, with Poisson cumulative distribution) from prior observations (most of them are assumed to be errors).
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToAnnotationCountsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToCountsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToReadSetMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactAlignmentToTranscriptCountsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactFileStatsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToFastaMode.OutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompactToSAMMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CompareAlignmentToGenomeMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/CompareGroupsVCFOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataInput.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDataOutput.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundDirectoryEntry.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileTool.PROGRAM_MODE.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/CompoundFileWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/CompressedRead.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeCountInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeStartCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/ComputeWeightCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatAlignmentReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateAlignmentMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ConcatenateCompactReadsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ConcatenatePermutations.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/ConstantAccumulator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConversionConfig.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/ConvertSamBAMReadToGobyAlignment.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/CountArchiveToPeakAnnotationsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdapterI.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/CountBinningAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/CountCalculator.html...
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java:56: warning: Tag @see: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder(MG4J).
[WARNING] * @see it.unimi.dsi.mg4j.io.ArithmeticDecoder (MG4J).
[WARNING] ^
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java:33: warning: Tag @see: reference not found: it.unimi.dsi.mg4j.io.ArithmeticDecoder(MG4J)
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[WARNING] ^
[WARNING] Date: 1/15/12
[WARNING] Time: 11:02 AM
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: Tag @link: reference not found: #BITS
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:60: warning: @return tag cannot be used in method with void return type.
[WARNING] void flush(InputBitStream ibs) throws IOException;
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: Tag @link: reference not found: #BITS
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[WARNING] ^
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: Tag @link: reference not found: #BITS
[WARNING] * the call, exactly {@link #BITS} excess bits will be present in the
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: Tag @link: reference not found: #BITS
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:51: warning: Tag @link: reference not found: #BITS
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoderI.java:65: warning: Tag @link: reference not found: #BITS
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[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FoldChangeMagnitudeCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/FormatConfigurator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/FormatFieldCounter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF2.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/FormatIndelVCF3.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightAnnotationCount.FormulaChoice.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FormulaWeightCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/FrequencyTable.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/FromToFreq.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/GCProportionWeight.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/GenericToolsDriver.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/GeneTranscriptRelationships.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/GenomeAlignmentTargetMapper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/GenomeDebugHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/GenomicRange.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/GenotypeFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/GenotypePredictor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/GenotypesOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/GobyAlignmentReaderFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/GobyConfiguration.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:72: warning: Tag @see: reference not found: org.campagnelab.goby.aligners.LastagAligner
[WARNING] * @see org.campagnelab.goby.aligners.LastagAligner
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:79: warning: Tag @see: reference not found: org.campagnelab.goby.aligners.LastAligner
[WARNING] * @see org.campagnelab.goby.aligners.LastAligner
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:87: warning: Tag @see: reference not found: org.campagnelab.goby.aligners.BWAAligner
[WARNING] * @see org.campagnelab.goby.aligners.BWAAligner
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/config/GobyConfiguration.java:95: warning: Tag @see: reference not found: org.campagnelab.goby.aligners.GSnapAligner
[WARNING] * @see org.campagnelab.goby.aligners.GSnapAligner
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/GobyDriver.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/GobyException.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobyQuickSeqvar.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/GobyRengine.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/exception/GobyRuntimeException.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobySamRecord.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/GobySamSegment.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/GobyVersion.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/GrepReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/GroupAssociations.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/GroupComparison.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/GZipChunkCodec.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/GzipOutputStreamWithCustomLevel.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/HeaderUtil.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/HeptamerInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HeptamerWeight.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/HeptamerWeightsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/HiCMerge.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.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] /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] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/methylation/HitBoundedPriorityQueue.java:131: warning: Tag @link: reference not found: edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore
[WARNING] * @return the next {@link edu.cornell.med.icb.tissueinfo.similarity.TranscriptScore}.
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/HTSJdkReaderFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/HTSJDKReaderImpl.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec1.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/HybridChunkCodec2.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/IndelCountOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/InferSexFromAlignmentsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/InfoForTarget.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/InfoOutput.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeColumns.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeDouble.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/InformativeNonZeroNonNaN.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Interval.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/InvalidChecksumException.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/IOUtil.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/IsDone.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateAlignments.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/IterateAlignmentsCodeSample.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignments.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/IterateSortedAlignmentsListImpl2.PositionBaseInfo2.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/IterateSortedAlignmentsToPileup.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/KnownIndelSet.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/LastParser.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/LastToCompactMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/LeftOverFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/LinearBinningStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/LocalSortProcessor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log10BinningStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Log2BinningStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/Log2FoldChangeCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/LogGCCorrectionWeight.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LoggingOutputStream.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LogIsConfigured.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/LongNamedCounter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/MakeBisulfiteFastaExample.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MaxCombinator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/MedianCombinator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/Merge.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MergeCompactAlignmentsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/MergeIndelFrom.SplitIndel.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MessageChunksWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationData.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylationFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/MethylationRateDifferenceStatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRateVCFOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationRegion.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/MethylationRegionsOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSimilarityMatch.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSite.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylationSiteIterator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylCountInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProvider.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderFromRegionsOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MethylCountProviderTestSupport.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/MethylRateInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/MethylSimilarityScan.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/MethylStats.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/MethylStatsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/MinCombinator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/ModifyAlignmentsCodeSample.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/MotifMatcher.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/MoveToFrontCoder.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<'
[WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:42: warning: invalid input: '<'
[WARNING] * @param symbol Symbol to encode with move to front (precondition: 0<= symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:43: warning: invalid input: '<'
[WARNING] * @return encoded symbol (post-condition: 0<= encoded-symbol <numberOfSymbols).
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/MoveToFrontCoder.java:43: warning: invalid input: '<'
[WARNING] * @return encoded symbol (post-condition: 0<= encoded-symbol <numberOfSymbols).
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/MultiReads.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/NamedCounters.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReader.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReader.java:258: warning: invalid input: '<'
[WARNING] * positions p are startPosition <= p < endPosition
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/NonAmbiguousAlignmentReaderFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/NoOpPermutationReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/NormalizationMethod.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/NotCompressedChunkCodec.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/NoUpgradeAlignmentReaderFactory.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/NullChunkCodec.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/NullResettableObjectPool.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/ObservationWriter.TypeOfPair.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/ObservedIndel.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/OffsetCountsReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/OneBinStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/OutputInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/OutputInfoFromWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/OverlapResult.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/ParseAlignmentEntriesCodeSample.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/ParseAlignmentEntriesWithIndexCodeSample.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/ParseReadsCodeSample.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PassThroughStatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/Peak.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/PeakAggregator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationReaderInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/PermutationWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/PicardFastaIndexedSequence.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/PlantIndels.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/PositionAdapter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/PositionBaseInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/PositionFacadeAlignmentReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/PositionToBasesMap.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/PostBarcodeMatcher.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/PreBarcodeMatcher.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/Predictor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/PrintWeights.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/ProtobuffCollectionHandler.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/ProtoHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestMciProviderStatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&rct'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&q'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&esrc'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&source'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&cd'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&cts'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&ved'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&url'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&ei'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&usg'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/algorithm/dmr/PTestStatisticAdaptor.java:24: warning: invalid input: '&sig2'
[WARNING] * See http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cts=1331678933809&ved=0CCYQFjAA&url=http%3A%2F%2Facademic.brooklyn.cuny.edu%2Feconomic%2Ffriedman%2FTtesttwoproportionsWEB.doc&ei=0M5fT7fHGYPt0gH5iI3OBw&usg=AFQjCNHYNyIZGnOV2nN-vC0Sdb-BFuzf6Q&sig2=KXQ6_M-LCSOSq7dVw_O21A
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/PVAlueProvider.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/QFast.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/QualityEncoding.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java:41: warning: invalid input: '&'
[WARNING] * !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java:41: warning: invalid input: '<'
[WARNING] * !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/QualityScoreFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/QueryIndexPermutationInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/QueueResettableObjectPool.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/RandomAccessAnnotations.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceCache.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/RandomAccessSequenceTestSupport.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Range.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/Ranges.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByEnd.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Read.ReadSortByStart.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodec2.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadCodecImpl.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/ReaderFastaParser.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadGroupHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadIndexStats.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/ReadNameToIndex.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReadOriginInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadQualityStatsMode.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<'
[WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<'
[WARNING] * Number of reads skipped because of sampleFraction value < 1.0d.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<'
[WARNING] * Number of reads skipped because of sampleFraction value < 1.0d.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<'
[WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadSet.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadSetToTextMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsLoader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/ReadsToText.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsToTextWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReadsToWeightsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/ReadsWriterImpl.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ReadWithIndex.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/RealignmentProcessor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ReferenceLocation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/ReformatCompactReadsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/RegionAveragingWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RegionWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/RegisterThis.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/Release1_9_7_2.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveBasesMatchingIndelsGenotypeFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/RemoveIndelArtifactsFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/RenameWeights.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/RepositionableInputStream.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/Resettable.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/ResettableObjectPoolInterface.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/RpkmLikeNormalizationMethod.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/RunParallelMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparison.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:233: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setCountComparisonFailures(final boolean countComparisonFailures) {
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparison.java:275: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setAllowSourceNs(boolean allowSourceNs) {
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamComparisonInterface.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/SamComparisonInterface.java:130: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setAllowSourceNs(boolean allowSourceNs);
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMComparisonMode.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java:214: warning: @return tag cannot be used in method with void return type.
[WARNING] public void setCheckMate(final boolean checkMate) {
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SamExtractReadsMode.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<'
[WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java:44: warning: invalid input: '<'
[WARNING] * WARNING: If the file contains pairs, the source SAM/BAM file >>MUST<< be sorted by read name.
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamPerPositionComparison.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleCountCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/SampleCountInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SamplePair.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/SamplePairEnumerator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SampleQualityScoresMode.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java:176: warning: invalid input: '<'
[WARNING] * Set to <= 0 to process the entire file.
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/SampleStats.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/SampleTotalCount.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SamRecordGenomicPositionComparator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SAMRecordIterable.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/SamRecordParser.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/SamSequenceVariation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactOldMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/ScanReferenceSequence.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/Segment.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&'
[WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '&'
[WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end;
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/data/Segment.java:137: warning: invalid input: '<'
[WARNING] * Determine if the segment overlaps with position. This method evaluates to position>=start && position<=end;
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceBaseInformationOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceBaseInformationWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceDigests.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/SequenceEncoder.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/SequenceSegmentInformationWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SequenceVariationOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.ReadIndexInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SequenceVariationPool.Variation.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStats2Mode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SequenceVariationStatsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/SimulateBisulfiteReads.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SimulateReadsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SitesInFixedWindow.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToListIterator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/SkipToSortedReader.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SlidingCountArray.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/SmallAndLog10BinningStrategy.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/SomaticPredictor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/SomaticVariationOutputFormat.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/Sort1Mode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SortedAnnotations.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/SortIterateAlignments.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SortMode.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/SortMode.java:142: warning: invalid input: '<'
[WARNING] * Set to < 0 for auto-detect number of cores.
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplicedSamHelper.Limits.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitCompactReadsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitFastaMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SplitTranscriptsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat3StatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat4StatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5MciProviderStatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/Stat5StatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorBaseQuality.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistancesToReadVariations.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToEndOfRead.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorDistanceToStartOfRead.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorInsertSizes.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorNumVariationsInRead.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorPairFlags.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryAlignedLength.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorQueryPosition.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorReadMappingQuality.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/StatAccumulatorTargetAlignedLength.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/StatisticAdaptor.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/StatisticComparator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/StatsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/StrandBiasFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/StreamSignal.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/SubSequenceMotifMatcher.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/SuggestPositionSlicesMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/SummedCombinator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TabToColumnInfoMode.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyBasesMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TallyReadsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TestRConnectionMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/TestSkipTo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Timer.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptBestScoreAlignmentFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/TranscriptsAlignmentFilter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/TrimMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TSVWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/TTestCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/UnboundedFifoPool.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/UnionDumpIterator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/UpgradeMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/UpgradeModeCore.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/UpgradeTo1_9_6.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.FromTo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/Variant.GobyIndelFromVCF.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapCreator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/VariantMapHelper.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFCompareMode.VCFPosition.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.html...
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/readers/vcf/VCFParser.java:179: warning: invalid input: '<'
[WARNING] * Set to <= 0 to scan the entire file. This must be set before calling readHeader() for the value to be used.
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/VCFParser.SyntaxException.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFSubsetMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToGenotypeMapMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VCFToKnownIndelsMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VcfToTabMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/VCFWriter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/VersionMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/WarningCounter.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/WeightCalculator.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WeightParameters.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/WeightsInfo.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/WiggleWindow.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/WithinGroupVariabilityMode.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/algorithm/dmr/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/compression/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/ranges/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/data/xml/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/dsv/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/algorithmic/indels/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/filters/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/htsjdk/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/perms/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/alignments/processors/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/baseinfo/package-summary.html...
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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/cli/package-tree.html...
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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/config/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/counts/compound/package-tree.html...
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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-summary.html...
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[WARNING] public final double getDenominator(final DifferentialExpressionCalculator differentialExpressionCalculator,
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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/AnnotationsToCountsMode.html...
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[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] ^
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[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/methylation/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/core/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/dsv/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/modes/formats/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/parsers/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/predictions/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/R/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/sam/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/readers/vcf/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/reads/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/stats/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/barcode/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/commits/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/dynoptions/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/motifs/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/util/pool/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/org/campagnelab/goby/xml/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/samples/package-use.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/overview-tree.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/deprecated-list.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/index.html...
[WARNING] Building index for all classes...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/allclasses-index.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/allpackages-index.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/index-all.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] /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] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:216: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:186: warning: invalid input: '<'
[WARNING] * Get the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:193: warning: invalid input: '<'
[WARNING] * Number of reads observed because of sampleFraction value < 1.0d. If sampleFraction == 1.0d
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/ReadQualityStatsMode.java:185: warning: invalid input: '<'
[WARNING] * Number of reads skipped because of sampleFraction value < 1.0d.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:364: warning: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:388: warning: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/core/TabToColumnInfoModeCore.java:224: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java:194: warning: invalid input: '<'
[WARNING] * Set the number of input lines to read or set to <= 0 to read the entire file.
[WARNING] ^
[WARNING] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/R/FisherExact.java:340: warning: Tag @link: reference not found: gominer.Fisher#fisher(int, int, int, int)
[WARNING] * {@link gominer.Fisher#fisher(int, int, int, int)}.
[WARNING] ^
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/overview-summary.html...
[WARNING] Generating /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/apidocs/help-doc.html...
[WARNING] 91 warnings
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-distribution-3.3.1-javadoc.jar
[INFO] 
[INFO] --- maven-assembly-plugin:3.4.2:single (make-assembly) @ goby-distribution ---
[INFO] Reading assembly descriptor: assembly/assembly.xml
[INFO] Building jar: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/goby-bin.jar
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO] 
[INFO] Goby Framework ..................................... SUCCESS [  0.057 s]
[INFO] Goby I/O ........................................... SUCCESS [ 26.718 s]
[INFO] Goby Full Distribution ............................. SUCCESS [ 29.254 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  56.175 s
[INFO] Finished at: 2025-02-14T02:30:02+14:00
[INFO] ------------------------------------------------------------------------
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2'
# Create a symlink to the directory with test data for tests run from the
# goby-distribution directory.
ln -s ../test-data goby-distribution/test-data
# The test-results directory should exist because test classes will write inside.
if [ ! -e test-results ]; then mkdir test-results/; fi
# Putting the JRI location in the path, as indicated in GobyRengine.java.
# Also indicating R_HOME, as found in http://rforge.net/JRI/.
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/lib/R/site-library/rJava/jri" && \
        export R_HOME="/usr/lib/R" && \
        dh_auto_test --no-parallel
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode test
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
[WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Goby Framework                                                     [pom]
[INFO] Goby I/O                                                           [jar]
[INFO] Goby Full Distribution                                             [jar]
[INFO] 
[INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
[INFO] Building Goby Framework 3.3.1                                      [1/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
[INFO] Building Goby I/O 3.3.1                                            [2/3]
[INFO] --------------------------------[ jar ]---------------------------------
[WARNING] The artifact org.apache.maven.plugins:maven-resources-plugin:jar:2.6 has been relocated to org.apache.maven.plugins:maven-resources-plugin:jar:3.3.0
[WARNING] The artifact org.apache.maven.plugins:maven-surefire-plugin:jar:2.12.4 has been relocated to org.apache.maven.plugins:maven-surefire-plugin:jar:2.22.3
[INFO] 
[INFO] --- build-helper-maven-plugin:3.3.0:add-source (add-classes) @ goby-io ---
[INFO] Source directory: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/generated-sources added.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-java-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (exec-python-cpp-protoc) @ goby-io ---
[INFO] Executing tasks
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-io ---
[INFO] Copying 2 resources
[INFO] Copying 1 resource
[INFO] Copying 1 resource
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-io ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 260 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/dynoptions/DynamicOptionRegistry.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/../goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-antrun-plugin:3.1.0:run (default) @ goby-io ---
[WARNING] Parameter tasks is deprecated, use target instead
[INFO] Executing tasks
[INFO]      [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2
[INFO]      [copy] Copying 1 file to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/target/classes
[INFO] Executed tasks
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ goby-io ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-io ---
[INFO] No sources to compile
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-io ---
[INFO] No tests to run.
[INFO] 
[INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
[INFO] Building Goby Full Distribution 3.3.1                              [3/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:resources (default-resources) @ goby-distribution ---
[INFO] Copying 3 resources
[INFO] Copying 72 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:compile (default-compile) @ goby-distribution ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 525 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/classes
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionToBasesMap.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java uses or overrides a deprecated API that is marked for removal.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsToTextWriter.java: Recompile with -Xlint:removal for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/main/java/org/campagnelab/goby/util/VariantMapHelper.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-resources-plugin:3.3.0:testResources (default-testResources) @ goby-distribution ---
[INFO] skip non existing resourceDirectory /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.10.1:testCompile (default-testCompile) @ goby-distribution ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 120 source files to /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/target/test-classes
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Some input files use or override a deprecated API.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/TestQFast.java: Recompile with -Xlint:deprecation for details.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Some input files use unchecked or unsafe operations.
[INFO] /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/src/test/java/org/campagnelab/goby/algorithmic/algorithm/dmr/TestDeNovoDMRfinder.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.3:test (default-test) @ goby-distribution ---
[INFO] 
[INFO] -------------------------------------------------------
[INFO]  T E S T S
[INFO] -------------------------------------------------------
[INFO] Running TestSuite
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/usr/share/java/slf4j-simple.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven-repo/ch/qos/logback/logback-classic/debian/logback-classic-debian.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/usr/share/java/logback-classic.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.SimpleLoggerFactory]
[Thread-0] INFO org.campagnelab.goby.R.RLoggerMainLoopCallback - 

[Thread-0] INFO org.campagnelab.goby.R.RLoggerMainLoopCallback - R version 4.2.2 Patched (2022-11-10 r83330) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)


[Thread-0] INFO org.campagnelab.goby.R.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.


[Thread-0] INFO org.campagnelab.goby.R.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.


[Thread-0] INFO org.campagnelab.goby.R.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.


original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGTGT 
original G----GTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: G 
original GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT mapped: GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGT 
original G--GTGTGTGTGTGTGTGTGTGTGTGTGTGCGTTG mapped: GGT 
qPhred=1
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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

[main] WARN org.campagnelab.goby.GobyVersion - Version number UNKNOWN not recognized. Assuming this version is the most recent.
 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[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=10000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=9
[main] WARN org.campagnelab.goby.compression.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
[main] WARN org.campagnelab.goby.compression.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
[main] WARN org.campagnelab.goby.compression.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
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] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49806.6 for sample B-7
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 47698.4 for sample B-3
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 95792.0 for sample A-3
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 102117 for sample A-12
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49147.7 for sample B-15
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 52112.4 for sample B-14
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48554.8 for sample B-11
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 101919 for sample A-17
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 50794.8 for sample B-2
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48225.4 for sample B-10
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98427.3 for sample A-16
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48291.3 for sample B-8
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 50399.5 for sample B-4
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98624.9 for sample A-2
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 102841 for sample A-0
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48686.6 for sample B-6
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97504.9 for sample A-9
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99217.8 for sample A-8
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 95923.8 for sample A-5
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99086.1 for sample A-4
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97175.5 for sample A-6
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 96253.2 for sample A-7
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49279.5 for sample B-5
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 100272 for sample A-10
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98822.6 for sample A-14
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49411.3 for sample B-9
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97768.4 for sample A-1
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48225.4 for sample B-0
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49411.3 for sample B-12
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48423.1 for sample B-13
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 100535 for sample A-19
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 99876.7 for sample A-18
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 98624.9 for sample A-15
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49477.2 for sample B-1
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 97900.2 for sample A-13
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 100931 for sample A-11
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49806.6 for sample B-16
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48423.1 for sample B-17
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 49477.2 for sample B-19
[main] INFO org.campagnelab.goby.stats.BullardUpperQuartileNormalization - normalization denominator 48620.7 for sample B-18
Creating base test directory: test-results/stats-writer
allele: A ref: [CC] alt: [T][main] INFO org.campagnelab.goby.stats.FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
[main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
[main] INFO org.campagnelab.goby.stats.FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
[main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
[main] INFO org.campagnelab.goby.stats.FDRAdjustment - Trying to perform FDR adjustment for statistic t-test-P-value
[main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic t-test-P-value was found, FDR adjustment executed.
[main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic t-test-P-value-Bonferroni-adjusted was found, FDR adjustment executed.
[main] INFO org.campagnelab.goby.stats.FDRAdjustment - Trying to perform FDR adjustment for statistic another-p-value
[main] INFO org.campagnelab.goby.stats.FDRAdjustment - ... statistic another-p-value was found, FDR adjustment executed.
[main] INFO org.campagnelab.goby.stats.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 [0.9953184599151038, 0.5006510400291034, -0.006769893822425353, -0.998122717478194, 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 16 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 16 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 16 threads.
[main] INFO org.campagnelab.goby.cli.DoInParallel - Executing on 16 threads.
##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=<ID=p-value1,Number=1,Type=Float,Description="A P-value">
##INFO=<ID=p-value2,Number=1,Type=Float,Description="A P-value">
##INFO=<ID=#Cm_Group[Group_1],Number=1,Type=Float,Description="Some count">
##FORMAT=<ID=Zygosity,Number=1,Type=String,Description="Zygosity">
##FORMAT=<ID=Another,Number=1,Type=String,Description="Another">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SampleA	SampleB

[main] INFO org.campagnelab.goby.alignments.IterateSortedAlignments - Alignment contains 1 reference sequences
                                               1/1 ..T

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
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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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

TTC[27]->CGT[27] / qual=1:2:3
A[15]->G[20] / qual=20
A[15]->G[20] / qual=20
Processing test-data/sample-qual-scores/30reads.fa
Processed 0 read entries.
Min quality score: 2147483647
Max quality score: -2147483648
Avg quality score: 0
Probable quality encoding scheme: fasta
Processing test-data/sample-qual-scores/30reads.fq
Processed 30 read entries.
Min quality score: 69
Max quality score: 98
Avg quality score: 94
Probable quality encoding scheme: Illumina/Solexa
field CHROM value: 0
field POS value: 145497099
field ID value: .
field REF value: A
field ALT value: G
field QUAL value: 17.1
field FILTER value: .
field INFO[DP] value: 2
field INFO[DP4] value: 0,0,2,0
field INFO[MQ] value: 25
field INFO[FQ] value: -30.8
field INFO[AF1] value: 0.9999
field INFO[CI95] value: 0.5,1
field INFO[PV4] value: 
field INFO[INDEL] value: INDEL
field INFO[PC2] value: 3,3
field INFO[PCHI2] value: 0.752
field INFO[QCHI2] value: 1
field INFO[RP] value: 
field FORMAT[GT] value: 
field FORMAT[GQ] value: 
field FORMAT[GL] value: 
field FORMAT[DP] value: 
field FORMAT[SP] value: 
field FORMAT[PL] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[GT] value: 1/1
field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] value: 42
field results/IPBKRNW/IPBKRNW-replicate.bam[GL] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[DP] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[SP] value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[PL] value: 25,3,0
field results/IPBKRNW/IPBKRNW-sorted.bam[GT] value: 1/1
field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] value: 42
field results/IPBKRNW/IPBKRNW-sorted.bam[GL] value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[DP] value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[SP] value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[PL] value: 25,3,0
field CHROM gfi:0 value: 0
field POS gfi:1 value: 145497099
field ID gfi:2 value: .
field REF gfi:3 value: A
field ALT gfi:4 value: G
field QUAL gfi:5 value: 17.1
field FILTER gfi:6 value: .
field FORMAT[GT] gfi:7 value: 
field FORMAT[GQ] gfi:8 value: 
field FORMAT[GL] gfi:9 value: 
field FORMAT[DP] gfi:10 value: 
field FORMAT[SP] gfi:11 value: 
field FORMAT[PL] gfi:12 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[GT] gfi:13 value: 1/1
field results/IPBKRNW/IPBKRNW-replicate.bam[GQ] gfi:14 value: 11
field results/IPBKRNW/IPBKRNW-replicate.bam[GL] gfi:15 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[DP] gfi:16 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[SP] gfi:17 value: 
field results/IPBKRNW/IPBKRNW-replicate.bam[PL] gfi:18 value: 015,4,0
field results/IPBKRNW/IPBKRNW-sorted.bam[GT] gfi:19 value: 1/1
field results/IPBKRNW/IPBKRNW-sorted.bam[GQ] gfi:20 value: 42
field results/IPBKRNW/IPBKRNW-sorted.bam[GL] gfi:21 value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[DP] gfi:22 value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[SP] gfi:23 value: 
field results/IPBKRNW/IPBKRNW-sorted.bam[PL] gfi:24 value: 25,3,0
Total logical entries written: 1
Total bytes written: 0
Average bytes/logical entry: 0.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 45
 peak : start :5 count :13 length :100010
 peak : start :100020 count :10 length :1
Appending count: 285 length: 2
Appending count: 36194 length: 10
Appending count: 13261 length: 9
Appending count: 44922 length: 9
Appending count: 975 length: 8
Appending count: 25753 length: 9
Appending count: 25843 length: 6
Appending count: 9163 length: 2
Appending count: 46212 length: 6
Appending count: 29600 length: 8
Appending count: 7145 length: 2
Appending count: 36315 length: 8
Appending count: 3495 length: 6
Appending count: 2445 length: 4
Appending count: 18663 length: 5
Appending count: 5352 length: 8
Appending count: 10239 length: 5
Appending count: 45891 length: 2
Appending count: 43664 length: 5
Appending count: 30745 length: 2
Appending count: 33964 length: 2
Appending count: 36478 length: 7
Appending count: 3282 length: 6
Appending count: 43616 length: 4
Appending count: 11415 length: 2
Appending count: 36997 length: 7
Appending count: 19026 length: 2
Appending count: 11655 length: 10
Appending count: 26307 length: 1
Appending count: 16185 length: 3
 position= 0 count= 285
 position= 1 count= 285
 position= 2 count= 36194
 position= 3 count= 36194
 position= 4 count= 36194
 position= 5 count= 36194
 position= 6 count= 36194
 position= 7 count= 36194
 position= 8 count= 36194
 position= 9 count= 36194
 position= 10 count= 36194
 position= 11 count= 36194
 position= 12 count= 13261
 position= 13 count= 13261
 position= 14 count= 13261
 position= 15 count= 13261
 position= 16 count= 13261
 position= 17 count= 13261
 position= 18 count= 13261
 position= 19 count= 13261
 position= 20 count= 13261
 position= 21 count= 44922
 position= 22 count= 44922
 position= 23 count= 44922
 position= 24 count= 44922
 position= 25 count= 44922
 position= 26 count= 44922
 position= 27 count= 44922
 position= 28 count= 44922
 position= 29 count= 44922
 position= 30 count= 975
 position= 31 count= 975
 position= 32 count= 975
 position= 33 count= 975
 position= 34 count= 975
 position= 35 count= 975
 position= 36 count= 975
 position= 37 count= 975
 position= 38 count= 25753
 position= 39 count= 25753
 position= 40 count= 25753
 position= 41 count= 25753
 position= 42 count= 25753
 position= 43 count= 25753
 position= 44 count= 25753
 position= 45 count= 25753
 position= 46 count= 25753
 position= 47 count= 25843
 position= 48 count= 25843
 position= 49 count= 25843
 position= 50 count= 25843
 position= 51 count= 25843
 position= 52 count= 25843
 position= 53 count= 9163
 position= 54 count= 9163
 position= 55 count= 46212
 position= 56 count= 46212
 position= 57 count= 46212
 position= 58 count= 46212
 position= 59 count= 46212
 position= 60 count= 46212
 position= 61 count= 29600
 position= 62 count= 29600
 position= 63 count= 29600
 position= 64 count= 29600
 position= 65 count= 29600
 position= 66 count= 29600
 position= 67 count= 29600
 position= 68 count= 29600
 position= 69 count= 7145
 position= 70 count= 7145
 position= 71 count= 36315
 position= 72 count= 36315
 position= 73 count= 36315
 position= 74 count= 36315
 position= 75 count= 36315
 position= 76 count= 36315
 position= 77 count= 36315
 position= 78 count= 36315
 position= 79 count= 3495
 position= 80 count= 3495
 position= 81 count= 3495
 position= 82 count= 3495
 position= 83 count= 3495
 position= 84 count= 3495
 position= 85 count= 2445
 position= 86 count= 2445
 position= 87 count= 2445
 position= 88 count= 2445
 position= 89 count= 18663
 position= 90 count= 18663
 position= 91 count= 18663
 position= 92 count= 18663
 position= 93 count= 18663
 position= 94 count= 5352
 position= 95 count= 5352
 position= 96 count= 5352
 position= 97 count= 5352
 position= 98 count= 5352
 position= 99 count= 5352
 position= 100 count= 5352
 position= 101 count= 5352
 position= 102 count= 10239
 position= 103 count= 10239
 position= 104 count= 10239
 position= 105 count= 10239
 position= 106 count= 10239
 position= 107 count= 45891
 position= 108 count= 45891
 position= 109 count= 43664
 position= 110 count= 43664
 position= 111 count= 43664
 position= 112 count= 43664
 position= 113 count= 43664
 position= 114 count= 30745
 position= 115 count= 30745
 position= 116 count= 33964
 position= 117 count= 33964
 position= 118 count= 36478
 position= 119 count= 36478
 position= 120 count= 36478
 position= 121 count= 36478
 position= 122 count= 36478
 position= 123 count= 36478
 position= 124 count= 36478
 position= 125 count= 3282
 position= 126 count= 3282
 position= 127 count= 3282
 position= 128 count= 3282
 position= 129 count= 3282
 position= 130 count= 3282
 position= 131 count= 43616
 position= 132 count= 43616
 position= 133 count= 43616
 position= 134 count= 43616
 position= 135 count= 11415
 position= 136 count= 11415
 position= 137 count= 36997
 position= 138 count= 36997
 position= 139 count= 36997
 position= 140 count= 36997
 position= 141 count= 36997
 position= 142 count= 36997
 position= 143 count= 36997
 position= 144 count= 19026
 position= 145 count= 19026
 position= 146 count= 11655
 position= 147 count= 11655
 position= 148 count= 11655
 position= 149 count= 11655
 position= 150 count= 11655
 position= 151 count= 11655
 position= 152 count= 11655
 position= 153 count= 11655
 position= 154 count= 11655
 position= 155 count= 11655
 position= 156 count= 26307
 position= 157 count= 16185
 position= 158 count= 16185
 position= 159 count= 16185
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 
[main] WARN org.campagnelab.goby.counts.WiggleWindow - Not writing 101 7
[main] WARN org.campagnelab.goby.counts.WiggleWindow - Not writing 111 7
[main] WARN org.campagnelab.goby.counts.WiggleWindow - Not writing 131 8
[main] WARN org.campagnelab.goby.counts.WiggleWindow - Not writing 141 8
[main] WARN org.campagnelab.goby.counts.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=10,length=4)
 appending (count=1,length=0)
 appending (count=2,length=8)
Hello
 appending (count=10,length=4)
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 0
Total bytes written: 31
Average bytes/logical entry: Infinity
Min query index: 2147483647
Max query index: -2147483648
Number of queries: 2
Number of targets: 0
97
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 6
Total bytes written: 162
Average bytes/logical entry: 27.0
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
0
23
Setting quality threshold to 0.02
entry:query_index: 0
target_index: 0
position: 5
score: 5.0
matching_reverse_strand: false
query_length: 20
query_aligned_length: 20
target_aligned_length: 20
sequence_variations {
  to: "CTAG"
  from: "----"
  position: 10
  read_index: 10
}

entry:query_index: 1
target_index: 0
position: 5
matching_reverse_strand: false
query_length: 20
query_aligned_length: 20
target_aligned_length: 20
sequence_variations {
  to: "CTAG"
  from: "----"
  position: 10
  to_quality: "(((("
  read_index: 10
}

entry: query_index: 0
target_index: 0
position: 0
matching_reverse_strand: false
query_length: 10
query_aligned_length: 10
sequence_variations {
  to: "AAA"
  from: "---"
  position: 3
  read_index: 3
}

processing entry on target 0 at position 0 
processing entry on target 0 at position 5 
processing entry on target 1 at position 0 
processing entry on target 1 at position 5 
processing entry on target 4 at position 0 
processing entry on target 4 at position 5 
entry:query_index: 0
target_index: 0
position: 10
matching_reverse_strand: false
query_length: 50
query_aligned_length: 50
sequence_variations {
  to: "AAA"
  from: "---"
  position: 20
  read_index: 20
}

entry:query_index: 1
target_index: 0
position: 1
matching_reverse_strand: false
query_length: 50
query_aligned_length: 50
sequence_variations {
  to: "T"
  from: "A"
  position: 20
  read_index: 20
}

[main] WARN org.campagnelab.goby.compression.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
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.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
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] INFO org.campagnelab.goby.alignments.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
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
Processing queryIndex=8 with description '8 perfect start of ref'
Processing queryIndex=9 with description '9 perfect start of ref reverse strand'
Processing queryIndex=18 with description '18 mismatch at end x1, starting at -1'
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'
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=2
Total logical entries written: 7
Total bytes written: 219
Average bytes/logical entry: 31.285715
Min query index: 0
Max query index: 0
Number of queries: 1
Number of targets: 3
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000

[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.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
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
entry: score=30.0000 readOriginIndex=0 
entry: score=30.0000 readOriginIndex=0 
Scanned 2 entries
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
0
2
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.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
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.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
[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.
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.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
preparing 105
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.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.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.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
[main] INFO org.campagnelab.goby.alignments.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: 3ms; used/avail/free/total/max mem: 64.09M/16.79G/187.56M/251.66M/16.85G
[main] INFO org.campagnelab.goby.alignments.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
score: 20020.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 1999
position: 19992
score: 20021.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

[main] INFO org.campagnelab.goby.alignments.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.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.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.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.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.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
[main] INFO org.campagnelab.goby.alignments.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.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: 114.43M/16.74G/137.23M/251.66M/16.85G
[main] INFO org.campagnelab.goby.alignments.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.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] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
preparing 105
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.Merge - TMH third pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [2 items, ? items/s, 0.00 ns/item]; used/avail/free/total/max mem: 64.36M/16.79G/187.30M/251.66M/16.85G
found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 3999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 3999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 3999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 3999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 3999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 3999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 3999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 3999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
preparing 105
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.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.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.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
[main] INFO org.campagnelab.goby.alignments.AlignmentTooManyHitsReader - basename test-results/alignments/merge/transcript-101.tmh has no 'too many hits' information (test-results/alignments/merge/transcript-101.tmh does not exist). Assuming no queries have too many hits.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms [1 items, ? items/s, 0.00 ns/item]
[main] INFO org.campagnelab.goby.alignments.Merge - TMH fourth pass
Warning: could not find depth/max-length-of-match in too many hits information.
[main] INFO org.campagnelab.goby.alignments.Merge - Completed.
[main] INFO org.campagnelab.goby.alignments.Merge - Elapsed: 1ms; used/avail/free/total/max mem: 123.08M/16.73G/128.58M/251.66M/16.85G
[main] INFO org.campagnelab.goby.alignments.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
position: 2
score: 31.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 0
target_index: 2
position: 3
score: 31.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 4
position: 6
score: 30.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
preparing 105
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.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.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.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.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.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.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
[main] INFO org.campagnelab.goby.alignments.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.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: 151.05M/16.70G/100.61M/251.66M/16.85G
[main] INFO org.campagnelab.goby.alignments.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.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] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
preparing 105
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
Finding max number of reads...
Found input file with 2 target(s)
[main] INFO org.campagnelab.goby.alignments.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)
[main] INFO org.campagnelab.goby.alignments.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.
[main] INFO org.campagnelab.goby.alignments.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.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.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.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
[main] INFO org.campagnelab.goby.alignments.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.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: 2ms; used/avail/free/total/max mem: 176.61M/16.68G/75.05M/251.66M/16.85G
Second pass: writing the merged alignment.
[main] INFO org.campagnelab.goby.alignments.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.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
Average bytes/logical entry: 0.0
Min query index: 0
Max query index: 9
Number of queries: 10
Number of targets: 4
Percent aligned: 100.0
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
preparing 105
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.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.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.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
[main] INFO org.campagnelab.goby.alignments.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: 61.26M/16.79G/593.05M/654.31M/16.85G
[main] INFO org.campagnelab.goby.alignments.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
score: 40.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 1
position: 12
score: 41.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 1
position: 13
score: 42.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1
position: 14
score: 43.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1
position: 15
score: 44.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1
position: 16
score: 45.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1
position: 17
score: 46.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1
position: 18
score: 47.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1
position: 19
score: 48.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1
position: 20
score: 49.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
preparing 105
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.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 - 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: 119.98M/16.73G/534.33M/654.31M/16.85G
found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 3999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 3999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 3999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 3999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 3999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 3999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 3999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 3999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
preparing 105
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] WARN org.campagnelab.goby.compression.MessageChunksWriter - Using chunk-size=1000
[main] INFO org.campagnelab.goby.alignments.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.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.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.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.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.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
[main] INFO org.campagnelab.goby.alignments.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.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: 212.25M/16.64G/442.06M/654.31M/16.85G
[main] INFO org.campagnelab.goby.alignments.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.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
score: 20020.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 1999
position: 19992
score: 20021.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 1999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 1999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 1999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 1999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 1999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 1999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 1999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 1999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 0
target_index: 3999
position: 19991
score: 20020.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 1
target_index: 3999
position: 19992
score: 20021.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 2
target_index: 3999
position: 19993
score: 20022.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 3
target_index: 3999
position: 19994
score: 20023.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 4
target_index: 3999
position: 19995
score: 20024.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 5
target_index: 3999
position: 19996
score: 20025.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 6
target_index: 3999
position: 19997
score: 20026.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 7
target_index: 3999
position: 19998
score: 20027.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 8
target_index: 3999
position: 19999
score: 20028.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

found entry: query_index: 9
target_index: 3999
position: 20000
score: 20029.0
matching_reverse_strand: false
multiplicity: 1
query_length: 35

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

[main] INFO org.campagnelab.goby.util.barcode.TestPostBarcodeMatcher - Num matches = 200, Num Ambiguous = 0, Num no matches = 0
[main] INFO org.campagnelab.goby.util.barcode.TestPostBarcodeMatcher - Time to parse 8 million reads 0 seconds
[ {N:15} {///////////00//0010} {N:15} {00101111001101100101111101111111/0/} |Encoded in 80 bits
[ {N:15} {11111111111001100101100011111001011110011011001011111011111111} {0} {1} {1} {1} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->29 {N:15} {00101111001101100101111101111111101110000000000000000000000000} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} {0} | ->74decoding: 0
decoding: 4
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
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
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
[main] WARN org.campagnelab.goby.algorithmic.algorithm.EquivalentIndelRegionCalculator - Cannot determine sequence at position 600000000 of reference-index 2 
Annotations loaded
Annotations loaded
Annotations loaded
Annotations loaded
Annotations loaded
[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46, Time elapsed: 115.33 s - in TestSuite
[GobyRengine-ShutdownHook] INFO org.campagnelab.goby.R.GobyRengine - Shutdown hook is terminating R
[INFO] 
[INFO] Results:
[INFO] 
[WARNING] Tests run: 512, Failures: 0, Errors: 0, Skipped: 46
[INFO] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO] 
[INFO] Goby Framework ..................................... SUCCESS [  0.077 s]
[INFO] Goby I/O ........................................... SUCCESS [ 10.798 s]
[INFO] Goby Full Distribution ............................. SUCCESS [02:08 min]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:19 min
[INFO] Finished at: 2025-02-14T02:32:23+14:00
[INFO] ------------------------------------------------------------------------
make[1]: Leaving directory '/build/reproducible-path/libgoby-java-3.3.1+dfsg2'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install
	/usr/lib/jvm/default-java/bin/java -noverify -cp /usr/share/maven/boot/plexus-classworlds-2.x.jar -Dmaven.home=/usr/share/maven -Dmaven.multiModuleProjectDirectory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 -Dclassworlds.conf=/etc/maven/m2-debian.conf org.codehaus.plexus.classworlds.launcher.Launcher -s/etc/maven/settings-debian.xml -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo --batch-mode -Ddebian.dir=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian -Ddebian.package=libgoby-io-java -Dmaven.repo.local=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2/debian/maven-repo -Dinstall.to.usj=true org.debian.maven:debian-maven-plugin:2.6:install
OpenJDK 64-Bit Server VM warning: Options -Xverify:none and -noverify were deprecated in JDK 13 and will likely be removed in a future release.
[INFO] Scanning for projects...
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-distribution:jar:3.3.1
[WARNING] 'dependencies.dependency.systemPath' for org.rosuda.REngine:REngine:jar should use a variable instead of a hard-coded path /usr/lib/R/site-library/rJava/jri/JRI.jar @ line 227, column 16
[WARNING] 'dependencies.dependency.systemPath' for com.github.broadinstitute:picard:jar should use a variable instead of a hard-coded path /usr/share/java/picard.jar @ line 293, column 16
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: it.unimi.dsi:dsiutils:jar -> duplicate declaration of version debian @ line 295, column 15
[WARNING] 
[WARNING] Some problems were encountered while building the effective model for org.campagnelab.goby:goby-io:jar:3.3.1
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: com.google.protobuf:protobuf-java:jar -> duplicate declaration of version debian @ line 350, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.itadaki:bzip2:jar should use a variable instead of a hard-coded path /usr/share/java/jbzip2-0.9.1.jar @ line 391, column 16
[WARNING] 'build.plugins.plugin.(groupId:artifactId)' must be unique but found duplicate declaration of plugin org.apache.maven.plugins:maven-antrun-plugin @ line 291, column 12
[WARNING] 
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING] 
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING] 
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] Goby Framework                                                     [pom]
[INFO] Goby I/O                                                           [jar]
[INFO] Goby Full Distribution                                             [jar]
[INFO] 
[INFO] ----------------< org.campagnelab.goby:goby-framework >-----------------
[INFO] Building Goby Framework 3.3.1                                      [1/3]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ goby-framework ---
[INFO] Cleaning pom file: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libgoby-io-java --has-package-version
[INFO] 	--rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.publishedRules
[INFO] 
[INFO] --------------------< org.campagnelab.goby:goby-io >--------------------
[INFO] Building Goby I/O 3.3.1                                            [2/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ goby-io ---
[INFO] Cleaning pom file: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=libgoby-io-java
[INFO] 	--rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.publishedRules
[INFO] Install jar for goby-io into /usr/share/java
[INFO] 
[INFO] ---------------< org.campagnelab.goby:goby-distribution >---------------
[INFO] Building Goby Full Distribution 3.3.1                              [3/3]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- debian-maven-plugin:2.6:install (default-cli) @ goby-distribution ---
[INFO] Cleaning pom file: /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml.save with options:
[INFO] 	--keep-pom-version --package=goby-java
[INFO] 	--rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.rules
[INFO] 	--ignore-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.ignoreRules
[INFO] 	--published-rules=/build/reproducible-path/libgoby-java-3.3.1+dfsg2/debian/maven.publishedRules
[INFO] Install jar for goby-distribution into /usr/share/java
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for Goby Framework 3.3.1:
[INFO] 
[INFO] Goby Framework ..................................... SUCCESS [  0.405 s]
[INFO] Goby I/O ........................................... SUCCESS [  0.069 s]
[INFO] Goby Full Distribution ............................. SUCCESS [  0.064 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  0.708 s
[INFO] Finished at: 2025-02-14T02:32:25+14:00
[INFO] ------------------------------------------------------------------------
	mh_resolve_dependencies --non-interactive --offline --build -plibgoby-io-java --base-directory=/build/reproducible-path/libgoby-java-3.3.1\+dfsg2 --non-explore
Analysing pom.xml...
Analysing goby-distribution/pom.xml...
Checking the parent dependency in the sub project goby-distribution/pom.xml
Analysing goby-io/pom.xml...
Checking the parent dependency in the sub project goby-io/pom.xml
> dpkg --search /usr/share/maven-repo/org/rosuda/REngine/REngine/*/* 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/maven-repo/org/rosuda/REngine/REngine
Feb 14, 2025 2:32:31 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve
SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-distribution/pom.xml: Dependency not found org.rosuda.REngine:REngine:jar:debian
> dpkg --search /usr/share/maven-repo/org/itadaki/bzip2/*/* 
dpkg failed to execute successfully
Offline mode. Give up looking for package containing /usr/share/maven-repo/org/itadaki/bzip2
Feb 14, 2025 2:32:37 AM org.debian.maven.packager.DependenciesSolver$ToResolve resolve
SEVERE: Cannot resolve dependencies in /build/reproducible-path/libgoby-java-3.3.1+dfsg2/goby-io/pom.xml: Dependency not found org.itadaki:bzip2:jar:debian
ERROR:
goby-distribution/pom.xml: dependency is not packaged in the Maven repository for Debian: org.rosuda.REngine:REngine:debian
goby-io/pom.xml: dependency is not packaged in the Maven repository for Debian: org.itadaki:bzip2:debian
--------
Some problems were found in this project, exiting...
	mh_unpatchpoms -plibgoby-io-java
   dh_install
   jh_installjavadoc
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_lintian
   dh_perl
   dh_link
   jh_installlibs
   jh_classpath
   jh_manifest
   jh_exec
   jh_depends
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_installdeb
   dh_gencontrol
dpkg-gencontrol: warning: Depends field of package libgoby-io-java: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${shlibs:Depends} used, but is not defined
dpkg-gencontrol: warning: Depends field of package goby-java: substitution variable ${maven:Depends} used, but is not defined
dpkg-gencontrol: warning: Recommends field of package goby-java: substitution variable ${maven:OptionalDepends} used, but is not defined
dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${java:Depends} unused, but is defined
dpkg-gencontrol: warning: package libgoby-io-java: substitution variable ${maven:CompileDepends} unused, but is defined
dpkg-gencontrol: warning: package goby-java: substitution variable ${java:Depends} unused, but is defined
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'goby-java' in '../goby-java_3.3.1+dfsg2-9_all.deb'.
dpkg-deb: building package 'libgoby-io-java' in '../libgoby-io-java_3.3.1+dfsg2-9_all.deb'.
 dpkg-genbuildinfo --build=binary -O../libgoby-java_3.3.1+dfsg2-9_amd64.buildinfo
 dpkg-genchanges --build=binary -O../libgoby-java_3.3.1+dfsg2-9_amd64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
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/2185384/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/2185384/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/2185384 and its subdirectories
I: Current time: Fri Feb 14 02:32:46 +14 2025
I: pbuilder-time-stamp: 1739449966