Diff of the two buildlogs: -- --- b1/build.log 2024-12-15 18:44:38.166831953 +0000 +++ b2/build.log 2024-12-15 18:46:57.208492711 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sat Jan 17 13:06:26 -12 2026 -I: pbuilder-time-stamp: 1768698386 +I: Current time: Mon Dec 16 08:44:40 +14 2024 +I: pbuilder-time-stamp: 1734288280 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -36,53 +36,86 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22513/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/38106/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Dec 15 18:44 /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/38106/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/38106/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=6 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='9c501a9a2e1f408c8c2b6f5a637a7b41' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='22513' - PS1='# ' - PS2='> ' + INVOCATION_ID=c53e87f014ec4aaca45b05896dd0efe5 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=38106 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Mk2gXC3z/pbuilderrc_kiXy --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Mk2gXC3z/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' - SUDO_GID='111' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.Mk2gXC3z/pbuilderrc_Bktk --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Mk2gXC3z/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux infom08-i386 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/22513/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/38106/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -250,7 +283,7 @@ Get: 118 http://deb.debian.org/debian unstable/main i386 libjsoncpp-dev i386 1.9.6-3 [25.0 kB] Get: 119 http://deb.debian.org/debian unstable/main i386 libsmithwaterman0 i386 0.0+git20160702.2610e25-12+b2 [38.7 kB] Get: 120 http://deb.debian.org/debian unstable/main i386 libsmithwaterman-dev i386 0.0+git20160702.2610e25-12+b2 [43.4 kB] -Fetched 78.1 MB in 1s (60.9 MB/s) +Fetched 78.1 MB in 2s (47.8 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19952 files and directories currently installed.) @@ -750,7 +783,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/38106/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/38106/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && 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 > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -788,8 +825,8 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' --- Configuring done (0.4s) --- Generating done (0.0s) +-- Configuring done (1.9s) +-- Generating done (0.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -805,7 +842,7 @@ -- Build files have been written to: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu dh_auto_build - cd obj-i686-linux-gnu && make -j6 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -821,74 +858,44 @@ make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build +make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build +make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build +make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build +[ 1%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o +[ 3%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o +[ 4%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o +[ 7%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o +[ 7%] Building CXX object CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -[ 3%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -MF CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o.d -o CMakeFiles/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/IndelAssembly/IndelAssembly.cpp -[ 6%] Building CXX object CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o -[ 6%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o -[ 7%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/VariantCaller.cpp.o -/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/OrderedBAMWriter.cpp In file included from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain::optimal_path() [with T = unsigned int]': @@ -909,28 +916,58 @@ /usr/include/c++/14/bits/stl_iterator.h:455:5: note: declared here 455 | operator!=(const reverse_iterator<_Iterator>& __x, | ^~~~~~~~ -[ 33%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o +[ 24%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o +/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp +[ 26%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] + 36 | arma::set_stream_err1(null_ostream); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +In file included from /usr/include/armadillo:412, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: +/usr/include/armadillo_bits/debug.hpp:83:1: note: declared here + 83 | set_stream_err1(const std::ostream&) + | ^~~~~~~~~~~~~~~ +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] + 37 | arma::set_stream_err2(null_ostream); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +/usr/include/armadillo_bits/debug.hpp:92:1: note: declared here + 92 | set_stream_err2(const std::ostream&) + | ^~~~~~~~~~~~~~~ +[ 29%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/DiagnosticJSON.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)': 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directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' dh_auto_test - cd obj-i686-linux-gnu && make -j6 test ARGS\+=--verbose ARGS\+=-j6 + cd obj-i686-linux-gnu && make -j10 test ARGS\+=--verbose ARGS\+=-j10 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j6 +/usr/bin/ctest --force-new-ctest-process --verbose -j10 UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu @@ -1086,6 +1123,250 @@ 6: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils 6: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 6: Test timeout computed to be: 10000000 +test 7 + Start 7: tvcutils_prepare_hotspots_call + +7: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "prepare_hotspots" +7: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu +7: Test timeout computed to be: 10000000 +test 8 + Start 8: tvcutils_validate_bed_call + +8: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "validate_bed" +8: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu +8: Test timeout computed to be: 10000000 +test 9 + Start 9: tvcutils_unify_vcf_call + +9: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "unify_vcf" +9: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu +9: Test timeout computed to be: 10000000 +test 10 + Start 10: tvcassembly_call + +10: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcassembly +10: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu +10: Test timeout computed to be: 10000000 +6: +6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. +6: +6: Usage: tvcutils [options] +6: +6: Commands: +6: prepare_hotspots Convert BED or VCF file into a valid hotspot file +6: validate_bed Validate targets or hotspots file +6: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) +6: +7: +7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. +7: +7: Usage: tvcutils prepare_hotspots [options] +7: +7: General options: +7: -b,--input-bed FILE input is a hotspots BED file (either -b or -v required) +7: -v,--input-vcf FILE input is a hotspots VCF file (either -b or -v required) +7: -d,--output-bed FILE output left-aligned hotspots in BED format [none] +7: -o,--output-vcf FILE output is a hotspots VCF file. To be used as input to --hotspot-vcf argument of variant_caller_pipeline.py (recommended) [none] +7: -r,--reference FILE FASTA file containing reference genome (required) +7: -a,--left-alignment on/off perform left-alignment of indels [off] +7: -s,--allow-block-substitutions on/off do not filter out block substitution hotspots [on] +7: -u,--unmerged-bed FILE input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional) +7: +8: +8: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. +8: +8: Usage: tvcutils validate_bed [options] +8: +8: Input selection options (must provide one): +8: --target-regions-bed FILE input is a target regions BED file (required) +8: --hotspots-bed FILE input is a hotspots BED file (required) +8: +8: General options: +8: --reference FILE FASTA file containing reference genome (required) +8: --validation-log FILE log file for user-readable warning/error messages [stdout] +8: --meta-json FILE save validation and file statistics to json file [none] +8: --unmerged-detail-bed FILE output a valid unmerged BED. To be used as input to --primer-trim-bed argument of variant_caller_pipeline.py (recommended) [none] +8: --unmerged-plain-bed FILE output a valid merged BED. To be used as input to --region-bed argument of variant_caller_pipeline.py (recommended) [none] +8: --merged-detail-bed FILE output an (almost) valid bedDetail merged BED [none] +8: --merged-plain-bed FILE output a valid plain merged BED [none] +8: --effective-bed FILE output a valid effective BED [none] +8: +9: Parameter novel-tvc-vcf is required and empty. +9: +9: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. +9: +9: Usage: tvcutils unify_vcf [options] +9: +9: General options: +9: -t,--novel-tvc-vcf FILE small variants VCF file produced by TVC (required) +9: -i,--novel-assembly-vcf FILE long indels VCF file produced by TVCASSEMBLY (optional) +9: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) +9: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) +9: -f,--reference-fasta FILE FASTA file containing reference genome (required) +9: -b,--target-file FILE target regions BED file (optional) +9: -o,--output-vcf FILE output merged and annotated VCF or VCF.GZ file (required) +9: -j,--tvc-metrics FILE JSON file with tvc metrics (optional) +9: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok) +9: -m,--min-depth INT minimum coverage depth in GVCF output (optional) +9: + 1/10 Test #6: tvcutils_call .................................... Passed 0.02 sec + 2/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.02 sec + 3/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.02 sec + 4/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.02 sec +3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller +3: +3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf +3: hp-max-length = 8 (integer, builtin default) +3: sse-prob-threshold = 0.2 (double, builtin default) +3: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) +3: sse-relative-safety-level = 0.025 (double, builtin default) +3: do-snp-realignment = true (boolean, builtin default) +3: do-mnp-realignment = true (boolean, builtin default) +3: realignment-threshold = 1 (double, builtin default) +3: indel-as-hpindel = false (boolean, builtin default) +3: data-quality-stringency = 4 (double, builtin default) +3: read-rejection-threshold = 0.5 (double, builtin default) +3: use-position-bias = false (boolean, builtin default) +3: position-bias-ref-fraction = 0.05 (double, builtin default) +3: position-bias = 0.75 (double, builtin default) +3: position-bias-pval = 0.05 (double, builtin default) +3: downsample-to-coverage = 2000 (integer, builtin default) +3: tune-sbias = 0.01 (double, builtin default) +3: suppress-reference-genotypes = true (boolean, builtin default) +3: suppress-nocall-genotypes = true (boolean, builtin default) +3: suppress-no-calls = true (boolean, builtin default) +3: heal-snps = true (boolean, builtin default) +3: snp-min-cov-each-strand = 0 (integer, builtin default) +3: snp-min-variant-score = 10 (double, builtin default) +3: snp-min-allele-freq = 0.2 (double, builtin default) +3: snp-min-coverage = 6 (integer, builtin default) +3: snp-strand-bias = 0.95 (double, builtin default) +3: snp-strand-bias-pval = 1 (double, builtin default) +3: mnp-min-cov-each-strand = 0 (integer, builtin default) +3: mnp-min-variant-score = 10 (double, builtin default) +3: mnp-min-allele-freq = 0.2 (double, builtin default) +3: mnp-min-coverage = 6 (integer, builtin default) +3: mnp-strand-bias = 0.95 (double, builtin default) +3: mnp-strand-bias-pval = 1 (double, builtin default) +3: indel-min-cov-each-strand = 1 (integer, builtin default) +3: indel-min-variant-score = 10 (double, builtin default) +3: indel-min-allele-freq = 0.2 (double, builtin default) +3: indel-min-coverage = 15 (integer, builtin default) +3: indel-strand-bias = 0.85 (double, builtin default) +3: indel-strand-bias-pval = 1 (double, builtin default) +3: hotspot-min-cov-each-strand = 0 (integer, builtin default) +3: hotspot-min-variant-score = 10 (double, builtin default) +3: hotspot-min-allele-freq = 0.2 (double, builtin default) +3: hotspot-min-coverage = 6 (integer, builtin default) +3: hotspot-strand-bias = 0.95 (double, builtin default) +3: hotspot-strand-bias-pval = 1 (double, builtin default) +3: max-flows-to-test = 10 (integer, builtin default) +3: min-delta-for-flow = 0.1 (double, builtin default) +3: prediction-precision = 30 (double, builtin default) +3: outlier-probability = 0.01 (double, builtin default) +3: germline-prior-strength = 0 (double, builtin default) +3: heavy-tailed = 3 (integer, builtin default) +3: filter-unusual-predictions = 0.3 (double, builtin default) +3: soft-clip-bias-checker = 0.1 (double, builtin default) +3: filter-deletion-predictions = 100 (double, builtin default) +3: filter-insertion-predictions = 100 (double, builtin default) +3: max-detail-level = 0 (integer, builtin default) +3: shift-likelihood-penalty = 0.3 (double, builtin default) +3: minimum-sigma-prior = 0.085 (double, builtin default) +3: slope-sigma-prior = 0.0084 (double, builtin default) +3: sigma-prior-weight = 1 (double, builtin default) +3: k-zero = 3 (double, builtin default) +3: num-threads = 1 (integer, command line option) +3: num-variants-per-thread = 250 (integer, builtin default) +3: use-sse-basecaller = false (boolean, command line option) +3: do-json-diagnostic = false (boolean, builtin default) +3: do-minimal-diagnostic = false (boolean, builtin default) +3: process-input-positions-only = false (boolean, builtin default) +3: suppress-recalibration = true (boolean, builtin default) +3: resolve-clipped-bases = false (boolean, builtin default) +3: prefix-exclude = 6 +3: allow-indels = true (boolean, builtin default) +3: allow-snps = true (boolean, builtin default) +3: allow-mnps = true (boolean, builtin default) +3: allow-complex = false (boolean, builtin default) +3: left-align-indels = false (boolean, builtin default) +3: use-best-n-alleles = 2 (integer, builtin default) +3: use-input-allele-only = false (boolean, builtin default) +3: min-mapping-qv = 4 (integer, builtin default) +3: read-snp-limit = 10 (integer, builtin default) +3: read-max-mismatch-fraction = 1 (double, builtin default) +3: max-complex-gap = 1 (integer, builtin default) +3: gen-min-alt-allele-freq = 0.2 (double, builtin default) +3: gen-min-coverage = 6 (integer, builtin default) +3: gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) +3: override-limits = false (boolean, builtin default) +3: Limit check parameter hp-max-length: lim. 1 <= 8? OK! +3: Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! +3: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! +3: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! +3: Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! +3: Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! +3: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! +3: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! +3: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! +3: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! +3: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! +3: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! +3: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! +3: Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! +3: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! +3: Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! +3: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! +3: Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! +3: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! +3: Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! +3: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! +3: Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! +3: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! +3: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! +3: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! +3: Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! +3: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! +3: Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! +3: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! +3: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! +3: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! +3: Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! +3: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! +3: Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! +3: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! +3: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! +3: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! +3: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! +3: Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! +3: Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! +3: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! +3: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! +3: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! +3: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! +3: Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! +3: Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! +3: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! +3: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! +3: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! +3: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! +3: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! +3: Limit check parameter k-zero: lim. 0 <= 3? OK! +3: Limit check parameter num-threads: lim. 1 <= 1 <= lim. 128? OK! +3: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! +3: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! +3: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! +3: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! +3: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! +3: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! +3: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! +3: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! +3: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed +3: TargetsManager: 1 target(s) +3: TargetsManager: Trimming of AmpliSeq primers is enabled +3: SampleManager: Found 1 read group(s) and 1 sample(s). +3: SampleManager: Primary sample "85" (default) present in 1 read group(s) +3: TVC found a total of 1 different flow orders of max flow lengths: 500 1: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 1: 1: Usage: tvc [options] @@ -1210,6 +1491,7 @@ 1: --do-minimal-diagnostic on/off (devel) provide minimal read information for called variants [off] 1: --override-limits on/off (devel) disable limit-check on input parameters [off]. 1: + 5/10 Test #1: tvc_call ......................................... Passed 0.06 sec 2: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 2: 2: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf @@ -1364,321 +1646,9 @@ 2: SampleManager: Found 1 read group(s) and 1 sample(s). 2: SampleManager: Primary sample "85" (default) present in 1 read group(s) 2: TVC found a total of 1 different flow orders of max flow lengths: 500 -3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller -3: -3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf -3: hp-max-length = 8 (integer, builtin default) -3: sse-prob-threshold = 0.2 (double, builtin default) -3: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) -3: sse-relative-safety-level = 0.025 (double, builtin default) -3: do-snp-realignment = true (boolean, builtin default) -3: do-mnp-realignment = true (boolean, builtin default) -3: realignment-threshold = 1 (double, builtin default) -3: indel-as-hpindel = false (boolean, builtin default) -3: data-quality-stringency = 4 (double, builtin default) -3: read-rejection-threshold = 0.5 (double, builtin default) -3: use-position-bias = false (boolean, builtin default) -3: position-bias-ref-fraction = 0.05 (double, builtin default) -3: position-bias = 0.75 (double, builtin default) -3: position-bias-pval = 0.05 (double, builtin default) -3: downsample-to-coverage = 2000 (integer, builtin default) -3: tune-sbias = 0.01 (double, builtin default) -3: suppress-reference-genotypes = true (boolean, builtin default) -3: suppress-nocall-genotypes = true (boolean, builtin default) -3: suppress-no-calls = true (boolean, builtin default) -3: heal-snps = true (boolean, builtin default) -3: snp-min-cov-each-strand = 0 (integer, builtin default) -3: snp-min-variant-score = 10 (double, builtin default) -3: snp-min-allele-freq = 0.2 (double, builtin default) -3: snp-min-coverage = 6 (integer, builtin default) -3: snp-strand-bias = 0.95 (double, builtin default) -3: snp-strand-bias-pval = 1 (double, builtin default) -3: mnp-min-cov-each-strand = 0 (integer, builtin default) -3: mnp-min-variant-score = 10 (double, builtin default) -3: mnp-min-allele-freq = 0.2 (double, builtin default) -3: mnp-min-coverage = 6 (integer, builtin default) -3: mnp-strand-bias = 0.95 (double, builtin default) -3: mnp-strand-bias-pval = 1 (double, builtin default) -3: indel-min-cov-each-strand = 1 (integer, builtin default) -3: indel-min-variant-score = 10 (double, builtin default) -3: indel-min-allele-freq = 0.2 (double, builtin default) -3: indel-min-coverage = 15 (integer, builtin default) -3: indel-strand-bias = 0.85 (double, builtin default) -3: indel-strand-bias-pval = 1 (double, builtin default) -3: hotspot-min-cov-each-strand = 0 (integer, builtin default) -3: hotspot-min-variant-score = 10 (double, builtin default) -3: hotspot-min-allele-freq = 0.2 (double, builtin default) -3: hotspot-min-coverage = 6 (integer, builtin default) -3: hotspot-strand-bias = 0.95 (double, builtin default) -3: hotspot-strand-bias-pval = 1 (double, builtin default) -3: max-flows-to-test = 10 (integer, builtin default) -3: min-delta-for-flow = 0.1 (double, builtin default) -3: prediction-precision = 30 (double, builtin default) -3: outlier-probability = 0.01 (double, builtin default) -3: germline-prior-strength = 0 (double, builtin default) -3: heavy-tailed = 3 (integer, builtin default) -3: filter-unusual-predictions = 0.3 (double, builtin default) -3: soft-clip-bias-checker = 0.1 (double, builtin default) -3: filter-deletion-predictions = 100 (double, builtin default) -3: filter-insertion-predictions = 100 (double, builtin default) -3: max-detail-level = 0 (integer, builtin default) -3: shift-likelihood-penalty = 0.3 (double, builtin default) -3: minimum-sigma-prior = 0.085 (double, builtin default) -3: slope-sigma-prior = 0.0084 (double, builtin default) -3: sigma-prior-weight = 1 (double, builtin default) -3: k-zero = 3 (double, builtin default) -3: num-threads = 1 (integer, command line option) -3: num-variants-per-thread = 250 (integer, builtin default) -3: use-sse-basecaller = false (boolean, command line option) -3: do-json-diagnostic = false (boolean, builtin default) -3: do-minimal-diagnostic = false (boolean, builtin default) -3: process-input-positions-only = false (boolean, builtin default) -3: suppress-recalibration = true (boolean, builtin default) -3: resolve-clipped-bases = false (boolean, builtin default) -3: prefix-exclude = 6 -3: allow-indels = true (boolean, builtin default) -3: allow-snps = true (boolean, builtin default) -3: allow-mnps = true (boolean, builtin default) -3: allow-complex = false (boolean, builtin default) -3: left-align-indels = false (boolean, builtin default) -3: use-best-n-alleles = 2 (integer, builtin default) -3: use-input-allele-only = false (boolean, builtin default) -3: min-mapping-qv = 4 (integer, builtin default) -3: read-snp-limit = 10 (integer, builtin default) -3: read-max-mismatch-fraction = 1 (double, builtin default) -3: max-complex-gap = 1 (integer, builtin default) -3: gen-min-alt-allele-freq = 0.2 (double, builtin default) -3: gen-min-coverage = 6 (integer, builtin default) -3: gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) -3: override-limits = false (boolean, builtin default) -3: Limit check parameter hp-max-length: lim. 1 <= 8? OK! -3: Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! -3: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! -3: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! -3: Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! -3: Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! -3: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! -3: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! -3: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! -3: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! -3: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! -3: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! -3: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! -3: Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! -3: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -3: Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! -3: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! -3: Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! -3: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! -3: Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! -3: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -3: Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! -3: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! -3: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! -3: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! -3: Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! -3: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -3: Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! -3: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! -3: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! -3: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! -3: Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! -3: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -3: Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! -3: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! -3: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! -3: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! -3: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! -3: Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! -3: Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! -3: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! -3: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! -3: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! -3: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! -3: Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! -3: Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! -3: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! -3: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! -3: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! -3: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! -3: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! -3: Limit check parameter k-zero: lim. 0 <= 3? OK! -3: Limit check parameter num-threads: lim. 1 <= 1 <= lim. 128? OK! -3: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! -3: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! -3: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! -3: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! -3: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! -3: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -3: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! -3: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -3: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed -3: TargetsManager: 1 target(s) -3: TargetsManager: Trimming of AmpliSeq primers is enabled -3: SampleManager: Found 1 read group(s) and 1 sample(s). -3: SampleManager: Primary sample "85" (default) present in 1 read group(s) -3: TVC found a total of 1 different flow orders of max flow lengths: 500 -4: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller -4: -4: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf -4: hp-max-length = 8 (integer, parameters json file) -4: sse-prob-threshold = 1 (double, parameters json file) -4: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) -4: sse-relative-safety-level = 0.025 (double, builtin default) -4: do-snp-realignment = false (boolean, parameters json file) -4: do-mnp-realignment = false (boolean, parameters json file) -4: realignment-threshold = 0 (double, parameters json file) -4: indel-as-hpindel = false (boolean, parameters json file) -4: data-quality-stringency = 10 (double, parameters json file) -4: read-rejection-threshold = 0.5 (double, builtin default) -4: use-position-bias = false (boolean, parameters json file) -4: position-bias-ref-fraction = 0.05 (double, parameters json file) -4: position-bias = 0.75 (double, parameters json file) -4: position-bias-pval = 0.05 (double, parameters json file) -4: downsample-to-coverage = 2000 (integer, parameters json file) -4: tune-sbias = 0.01 (double, builtin default) -4: suppress-reference-genotypes = true (boolean, builtin default) -4: suppress-nocall-genotypes = true (boolean, builtin default) -4: suppress-no-calls = true (boolean, builtin default) -4: heal-snps = true (boolean, builtin default) -4: snp-min-cov-each-strand = 4 (integer, parameters json file) -4: snp-min-variant-score = 6 (double, parameters json file) -4: snp-min-allele-freq = 0.02 (double, parameters json file) -4: snp-min-coverage = 100 (integer, parameters json file) -4: snp-strand-bias = 0.95 (double, parameters json file) -4: snp-strand-bias-pval = 0.01 (double, parameters json file) -4: mnp-min-cov-each-strand = 4 (integer, parameters json file) -4: mnp-min-variant-score = 6 (double, parameters json file) -4: mnp-min-allele-freq = 0.02 (double, parameters json file) -4: mnp-min-coverage = 100 (integer, parameters json file) -4: mnp-strand-bias = 0.95 (double, parameters json file) -4: mnp-strand-bias-pval = 0.01 (double, parameters json file) -4: indel-min-cov-each-strand = 4 (integer, parameters json file) -4: indel-min-variant-score = 6 (double, parameters json file) -4: indel-min-allele-freq = 0.02 (double, parameters json file) -4: indel-min-coverage = 100 (integer, parameters json file) -4: indel-strand-bias = 0.9 (double, parameters json file) -4: indel-strand-bias-pval = 1 (double, parameters json file) -4: hotspot-min-cov-each-strand = 4 (integer, parameters json file) -4: hotspot-min-variant-score = 6 (double, parameters json file) -4: hotspot-min-allele-freq = 0.02 (double, parameters json file) -4: hotspot-min-coverage = 100 (integer, parameters json file) -4: hotspot-strand-bias = 0.95 (double, parameters json file) -4: hotspot-strand-bias-pval = 0.01 (double, parameters json file) -4: max-flows-to-test = 10 (integer, builtin default) -4: min-delta-for-flow = 0.1 (double, builtin default) -4: prediction-precision = 1 (double, parameters json file) -4: outlier-probability = 0.005 (double, parameters json file) -4: germline-prior-strength = 0 (double, builtin default) -4: heavy-tailed = 3 (integer, parameters json file) -4: filter-unusual-predictions = 0.12 (double, parameters json file) -4: soft-clip-bias-checker = 0.1 (double, builtin default) -4: filter-deletion-predictions = 0.2 (double, parameters json file) -4: filter-insertion-predictions = 0.2 (double, parameters json file) -4: max-detail-level = 0 (integer, builtin default) -4: shift-likelihood-penalty = 0.3 (double, builtin default) -4: minimum-sigma-prior = 0.085 (double, builtin default) -4: slope-sigma-prior = 0.0084 (double, builtin default) -4: sigma-prior-weight = 1 (double, builtin default) -4: k-zero = 3 (double, builtin default) -4: num-threads = 4 (integer, command line option) -4: num-variants-per-thread = 250 (integer, builtin default) -4: use-sse-basecaller = true (boolean, command line option) -4: do-json-diagnostic = false (boolean, builtin default) -4: do-minimal-diagnostic = false (boolean, builtin default) -4: process-input-positions-only = false (boolean, builtin default) -4: suppress-recalibration = false (boolean, parameters json file) -4: resolve-clipped-bases = false (boolean, builtin default) -4: prefix-exclude = 6 -4: allow-indels = true (boolean, parameters json file) -4: allow-snps = true (boolean, parameters json file) -4: allow-mnps = true (boolean, parameters json file) -4: allow-complex = false (boolean, parameters json file) -4: left-align-indels = false (boolean, builtin default) -4: use-best-n-alleles = 2 (integer, builtin default) -4: use-input-allele-only = false (boolean, builtin default) -4: min-mapping-qv = 4 (integer, parameters json file) -4: read-snp-limit = 10 (integer, parameters json file) -4: read-max-mismatch-fraction = 1 (double, parameters json file) -4: max-complex-gap = 1 (integer, builtin default) -4: gen-min-alt-allele-freq = 0.01 (double, parameters json file) -4: gen-min-coverage = 6 (integer, parameters json file) -4: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file) -4: override-limits = false (boolean, builtin default) -4: Limit check parameter hp-max-length: lim. 1 <= 8? OK! -4: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK! -4: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! -4: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! -4: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK! -4: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK! -4: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! -4: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! -4: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! -4: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! -4: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! -4: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! -4: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK! -4: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK! -4: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! -4: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK! -4: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! -4: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! -4: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK! -4: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK! -4: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! -4: Limit check parameter mnp-min-coverage: lim. 0 <= 100? OK! -4: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! -4: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! -4: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK! -4: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK! -4: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! -4: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK! -4: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= lim. 1? OK! -4: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! -4: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 4? OK! -4: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK! -4: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! -4: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? OK! -4: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! -4: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! -4: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! -4: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! -4: Limit check parameter prediction-precision: lim. 0.1 <= 1? OK! -4: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= lim. 1? OK! -4: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! -4: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! -4: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.12? OK! -4: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! -4: Limit check parameter filter-deletion-predictions: lim. 0 <= 0.2? OK! -4: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? OK! -4: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! -4: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! -4: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! -4: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! -4: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! -4: Limit check parameter k-zero: lim. 0 <= 3? OK! -4: Limit check parameter num-threads: lim. 1 <= 4 <= lim. 128? OK! -4: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! -4: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! -4: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! -4: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! -4: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! -4: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! -4: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! -4: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! -4: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed -4: TargetsManager: 1 target(s) -4: TargetsManager: Trimming of AmpliSeq primers is enabled - 1/10 Test #1: tvc_call ......................................... Passed 0.01 sec -test 7 - Start 7: tvcutils_prepare_hotspots_call - -7: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "prepare_hotspots" -7: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu -7: Test timeout computed to be: 10000000 -4: SampleManager: Found 1 read group(s) and 1 sample(s). -4: SampleManager: Primary sample "85" (default) present in 1 read group(s) -4: TVC found a total of 1 different flow orders of max flow lengths: 500 +2: Recalibration was detected from comment lines in bam file(s): +2: 1 unique blocks of recalibration info detected. +2: Loading systematic error contexts. 5: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 5: 5: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf @@ -1833,99 +1803,169 @@ 5: SampleManager: Found 1 read group(s) and 1 sample(s). 5: SampleManager: Primary sample "85" (default) present in 1 read group(s) 5: TVC found a total of 1 different flow orders of max flow lengths: 500 -6: -6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. -6: -6: Usage: tvcutils [options] -6: -6: Commands: -6: prepare_hotspots Convert BED or VCF file into a valid hotspot file -6: validate_bed Validate targets or hotspots file -6: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) -6: - 2/10 Test #6: tvcutils_call .................................... Passed 0.00 sec -test 8 - Start 8: tvcutils_validate_bed_call - -8: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "validate_bed" -8: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu -8: Test timeout computed to be: 10000000 -7: -7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. -7: -7: Usage: tvcutils prepare_hotspots [options] -7: -7: General options: -7: -b,--input-bed FILE input is a hotspots BED file (either -b or -v required) -7: -v,--input-vcf FILE input is a hotspots VCF file (either -b or -v required) -7: -d,--output-bed FILE output left-aligned hotspots in BED format [none] -7: -o,--output-vcf FILE output is a hotspots VCF file. To be used as input to --hotspot-vcf argument of variant_caller_pipeline.py (recommended) [none] -7: -r,--reference FILE FASTA file containing reference genome (required) -7: -a,--left-alignment on/off perform left-alignment of indels [off] -7: -s,--allow-block-substitutions on/off do not filter out block substitution hotspots [on] -7: -u,--unmerged-bed FILE input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional) -7: - 3/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.00 sec -test 9 - Start 9: tvcutils_unify_vcf_call - -9: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "unify_vcf" -9: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu -9: Test timeout computed to be: 10000000 -2: Recalibration was detected from comment lines in bam file(s): -2: 1 unique blocks of recalibration info detected. -2: Loading systematic error contexts. -8: -8: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. -8: -8: Usage: tvcutils validate_bed [options] -8: -8: Input selection options (must provide one): -8: --target-regions-bed FILE input is a target regions BED file (required) -8: --hotspots-bed FILE input is a hotspots BED file (required) -8: -8: General options: -8: --reference FILE FASTA file containing reference genome (required) -8: --validation-log FILE log file for user-readable warning/error messages [stdout] -8: --meta-json FILE save validation and file statistics to json file [none] -8: --unmerged-detail-bed FILE output a valid unmerged BED. To be used as input to --primer-trim-bed argument of variant_caller_pipeline.py (recommended) [none] -8: --unmerged-plain-bed FILE output a valid merged BED. To be used as input to --region-bed argument of variant_caller_pipeline.py (recommended) [none] -8: --merged-detail-bed FILE output an (almost) valid bedDetail merged BED [none] -8: --merged-plain-bed FILE output a valid plain merged BED [none] -8: --effective-bed FILE output a valid effective BED [none] -8: - 4/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.00 sec -test 10 - Start 10: tvcassembly_call - -10: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcassembly -10: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu -10: Test timeout computed to be: 10000000 -9: Parameter novel-tvc-vcf is required and empty. -9: -9: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. -9: -9: Usage: tvcutils unify_vcf [options] -9: -9: General options: -9: -t,--novel-tvc-vcf FILE small variants VCF file produced by TVC (required) -9: -i,--novel-assembly-vcf FILE long indels VCF file produced by TVCASSEMBLY (optional) -9: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) -9: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) -9: -f,--reference-fasta FILE FASTA file containing reference genome (required) -9: -b,--target-file FILE target regions BED file (optional) -9: -o,--output-vcf FILE output merged and annotated VCF or VCF.GZ file (required) -9: -j,--tvc-metrics FILE JSON file with tvc metrics (optional) -9: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok) -9: -m,--min-depth INT minimum coverage depth in GVCF output (optional) -9: -4: Recalibration was detected from comment lines in bam file(s): -4: 1 unique blocks of recalibration info detected. -4: Loading systematic error contexts. - 5/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.00 sec 5: Recalibration was detected from comment lines in bam file(s): 5: 1 unique blocks of recalibration info detected. 5: Loading systematic error contexts. +4: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller +4: +4: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf +4: hp-max-length = 8 (integer, parameters json file) +4: sse-prob-threshold = 1 (double, parameters json file) +4: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) +4: sse-relative-safety-level = 0.025 (double, builtin default) +4: do-snp-realignment = false (boolean, parameters json file) +4: do-mnp-realignment = false (boolean, parameters json file) +4: realignment-threshold = 0 (double, parameters json file) +4: indel-as-hpindel = false (boolean, parameters json file) +4: data-quality-stringency = 10 (double, parameters json file) +4: read-rejection-threshold = 0.5 (double, builtin default) +4: use-position-bias = false (boolean, parameters json file) +4: position-bias-ref-fraction = 0.05 (double, parameters json file) +4: position-bias = 0.75 (double, parameters json file) +4: position-bias-pval = 0.05 (double, parameters json file) +4: downsample-to-coverage = 2000 (integer, parameters json file) +4: tune-sbias = 0.01 (double, builtin default) +4: suppress-reference-genotypes = true (boolean, builtin default) +4: suppress-nocall-genotypes = true (boolean, builtin default) +4: suppress-no-calls = true (boolean, builtin default) +4: heal-snps = true (boolean, builtin default) +4: snp-min-cov-each-strand = 4 (integer, parameters json file) +4: snp-min-variant-score = 6 (double, parameters json file) +4: snp-min-allele-freq = 0.02 (double, parameters json file) +4: snp-min-coverage = 100 (integer, parameters json file) +4: snp-strand-bias = 0.95 (double, parameters json file) +4: snp-strand-bias-pval = 0.01 (double, parameters json file) +4: mnp-min-cov-each-strand = 4 (integer, parameters json file) +4: mnp-min-variant-score = 6 (double, parameters json file) +4: mnp-min-allele-freq = 0.02 (double, parameters json file) +4: mnp-min-coverage = 100 (integer, parameters json file) +4: mnp-strand-bias = 0.95 (double, parameters json file) +4: mnp-strand-bias-pval = 0.01 (double, parameters json file) +4: indel-min-cov-each-strand = 4 (integer, parameters json file) +4: indel-min-variant-score = 6 (double, parameters json file) +4: indel-min-allele-freq = 0.02 (double, parameters json file) +4: indel-min-coverage = 100 (integer, parameters json file) +4: indel-strand-bias = 0.9 (double, parameters json file) +4: indel-strand-bias-pval = 1 (double, parameters json file) +4: hotspot-min-cov-each-strand = 4 (integer, parameters json file) +4: hotspot-min-variant-score = 6 (double, parameters json file) +4: hotspot-min-allele-freq = 0.02 (double, parameters json file) +4: hotspot-min-coverage = 100 (integer, parameters json file) +4: hotspot-strand-bias = 0.95 (double, parameters json file) +4: hotspot-strand-bias-pval = 0.01 (double, parameters json file) +4: max-flows-to-test = 10 (integer, builtin default) +4: min-delta-for-flow = 0.1 (double, builtin default) +4: prediction-precision = 1 (double, parameters json file) +4: outlier-probability = 0.005 (double, parameters json file) +4: germline-prior-strength = 0 (double, builtin default) +4: heavy-tailed = 3 (integer, parameters json file) +4: filter-unusual-predictions = 0.12 (double, parameters json file) +4: soft-clip-bias-checker = 0.1 (double, builtin default) +4: filter-deletion-predictions = 0.2 (double, parameters json file) +4: filter-insertion-predictions = 0.2 (double, parameters json file) +4: max-detail-level = 0 (integer, builtin default) +4: shift-likelihood-penalty = 0.3 (double, builtin default) +4: minimum-sigma-prior = 0.085 (double, builtin default) +4: slope-sigma-prior = 0.0084 (double, builtin default) +4: sigma-prior-weight = 1 (double, builtin default) +4: k-zero = 3 (double, builtin default) +4: num-threads = 4 (integer, command line option) +4: num-variants-per-thread = 250 (integer, builtin default) +4: use-sse-basecaller = true (boolean, command line option) +4: do-json-diagnostic = false (boolean, builtin default) +4: do-minimal-diagnostic = false (boolean, builtin default) +4: process-input-positions-only = false (boolean, builtin default) +4: suppress-recalibration = false (boolean, parameters json file) +4: resolve-clipped-bases = false (boolean, builtin default) +4: prefix-exclude = 6 +4: allow-indels = true (boolean, parameters json file) +4: allow-snps = true (boolean, parameters json file) +4: allow-mnps = true (boolean, parameters json file) +4: allow-complex = false (boolean, parameters json file) +4: left-align-indels = false (boolean, builtin default) +4: use-best-n-alleles = 2 (integer, builtin default) +4: use-input-allele-only = false (boolean, builtin default) +4: min-mapping-qv = 4 (integer, parameters json file) +4: read-snp-limit = 10 (integer, parameters json file) +4: read-max-mismatch-fraction = 1 (double, parameters json file) +4: max-complex-gap = 1 (integer, builtin default) +4: gen-min-alt-allele-freq = 0.01 (double, parameters json file) +4: gen-min-coverage = 6 (integer, parameters json file) +4: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file) +4: override-limits = false (boolean, builtin default) +4: Limit check parameter hp-max-length: lim. 1 <= 8? OK! +4: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK! +4: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! +4: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! +4: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK! +4: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK! +4: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! +4: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! +4: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! +4: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! +4: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! +4: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! +4: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK! +4: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK! +4: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! +4: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK! +4: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! +4: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! +4: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK! +4: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK! +4: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! +4: Limit check parameter mnp-min-coverage: lim. 0 <= 100? OK! +4: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! +4: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! +4: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK! +4: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK! +4: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! +4: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK! +4: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= lim. 1? OK! +4: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! +4: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 4? OK! +4: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK! +4: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! +4: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? OK! +4: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! +4: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! +4: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! +4: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! +4: Limit check parameter prediction-precision: lim. 0.1 <= 1? OK! +4: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= lim. 1? OK! +4: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! +4: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! +4: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.12? OK! +4: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! +4: Limit check parameter filter-deletion-predictions: lim. 0 <= 0.2? OK! +4: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? OK! +4: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! +4: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! +4: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! +4: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! +4: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! +4: Limit check parameter k-zero: lim. 0 <= 3? OK! +4: Limit check parameter num-threads: lim. 1 <= 4 <= lim. 128? OK! +4: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! +4: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! +4: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! +4: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! +4: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! +4: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! +4: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! +4: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! +4: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed +4: TargetsManager: 1 target(s) +4: TargetsManager: Trimming of AmpliSeq primers is enabled +4: SampleManager: Found 1 read group(s) and 1 sample(s). +4: SampleManager: Primary sample "85" (default) present in 1 read group(s) +4: TVC found a total of 1 different flow orders of max flow lengths: 500 +4: Recalibration was detected from comment lines in bam file(s): +4: 1 unique blocks of recalibration info detected. +4: Loading systematic error contexts. +3: Recalibration was detected from comment lines in bam file(s): +3: 1 unique blocks of recalibration info detected. +3: Loading systematic error contexts. 10: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 10: 10: Usage: tvcassembly [options] @@ -1952,41 +1992,38 @@ 10: --relative_strand_bias FLOAT (stbias) Variants with strand bias above this are not reported [0.80]. 10: --output_mnv INT (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0]. 10: - 6/10 Test #10: tvcassembly_call ................................. Passed 0.00 sec -3: Recalibration was detected from comment lines in bam file(s): -3: 1 unique blocks of recalibration info detected. -3: Loading systematic error contexts. -4: Loaded. -2: Loaded. -5: Loaded. + 6/10 Test #10: tvcassembly_call ................................. Passed 0.05 sec 3: Loaded. -4: -4: -4: [tvc] Normal termination. Processing time: 0 seconds. +5: Loaded. +2: Loaded. +4: Loaded. +3: Recalibration model: suppressed +3: +3: +3: [tvc] Normal termination. Processing time: 1 seconds. 2: Recalibration model: suppressed 2: 2: -2: [tvc] Normal termination. Processing time: 0 seconds. +2: [tvc] Normal termination. Processing time: 1 seconds. 5: 5: -5: [tvc] Normal termination. Processing time: 0 seconds. -3: Recalibration model: suppressed -3: -3: -3: [tvc] Normal termination. Processing time: 0 seconds. - 7/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 0.67 sec - 8/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 0.67 sec - 9/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 0.68 sec -10/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 0.68 sec +5: [tvc] Normal termination. Processing time: 1 seconds. +4: +4: +4: [tvc] Normal termination. Processing time: 1 seconds. + 7/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 1.20 sec + 8/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 1.27 sec + 9/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.28 sec +10/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 1.39 sec 100% tests passed, 0 tests failed out of 10 -Total Test time (real) = 0.69 sec +Total Test time (real) = 1.41 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ - cd obj-i686-linux-gnu && make -j6 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2002,30 +2039,30 @@ -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' dh_installdocs dh_installchangelogs @@ -2040,13 +2077,13 @@ dh_strip -a dh_makeshlibs -a dh_shlibdeps -a -dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against libdisorder.so.0 (they use none of the library's symbols) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcutils were not linked against libdisorder.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_i386.deb'. +dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2054,12 +2091,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/38106/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/38106/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/22513 and its subdirectories -I: Current time: Sat Jan 17 13:07:36 -12 2026 -I: pbuilder-time-stamp: 1768698456 +I: removing directory /srv/workspace/pbuilder/38106 and its subdirectories +I: Current time: Mon Dec 16 08:46:56 +14 2024 +I: pbuilder-time-stamp: 1734288416