Diff of the two buildlogs: -- --- b1/build.log 2024-04-24 04:48:00.542099209 +0000 +++ b2/build.log 2024-04-24 04:49:19.630722399 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Apr 23 16:45:53 -12 2024 -I: pbuilder-time-stamp: 1713933953 +I: Current time: Wed May 28 01:11:03 +14 2025 +I: pbuilder-time-stamp: 1748344263 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -29,54 +29,86 @@ dpkg-source: info: applying use_debian_packaged_libs.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/11826/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3189/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-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 May 27 11:11 /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/3189/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3189/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=11 ' - DISTRIBUTION='trixie' - 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]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='4748f20828db43e6a44e95696279e559' - 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='11826' - PS1='# ' - PS2='> ' + INVOCATION_ID=751a6b3838dd4b13ba427f5625560e40 + 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=3189 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.l9kPqdeh/pbuilderrc_Jbio --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.l9kPqdeh/b1 --logfile b1/build.log metabat_2.15-4.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.l9kPqdeh/pbuilderrc_Trv6 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.l9kPqdeh/b2 --logfile b2/build.log metabat_2.15-4.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://213.165.73.152:3128 I: uname -a - Linux ionos12-i386 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.85-1 (2024-04-11) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 07:12 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/11826/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 24 13:35 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/3189/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -233,7 +265,7 @@ Get: 97 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-1+b2 [30.2 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-1+b2 [26.2 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 pkg-config i386 1.8.1-1+b2 [14.0 kB] -Fetched 74.1 MB in 1s (57.6 MB/s) +Fetched 74.1 MB in 1s (77.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal: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 ... 19876 files and directories currently installed.) @@ -565,8 +597,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Wed Apr 24 04:46:32 UTC 2024. -Universal Time is now: Wed Apr 24 04:46:32 UTC 2024. +Local time is now: Tue May 27 11:11:29 UTC 2025. +Universal Time is now: Tue May 27 11:11:29 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:i386 (1.83.0-2+b2) ... @@ -652,7 +684,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/metabat-2.15/ && 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 > ../metabat_2.15-4_source.changes +I: user script /srv/workspace/pbuilder/3189/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/3189/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/metabat-2.15/ && 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 > ../metabat_2.15-4_source.changes dpkg-buildpackage: info: source package metabat dpkg-buildpackage: info: source version 2.15-4 dpkg-buildpackage: info: source distribution unstable @@ -695,7 +731,7 @@ Boost libraries:/usr/lib/i386-linux-gnu/libboost_program_options.a/usr/lib/i386-linux-gnu/libboost_filesystem.a/usr/lib/i386-linux-gnu/libboost_system.a/usr/lib/i386-linux-gnu/libboost_graph.a/usr/lib/i386-linux-gnu/libboost_serialization.a/usr/lib/i386-linux-gnu/libboost_iostreams.a/usr/lib/i386-linux-gnu/libboost_regex.a Boost lib ver:1_83 Boost lib dir:/usr/lib/i386-linux-gnu --- Configuring done (3.0s) +-- Configuring done (2.0s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -711,7 +747,7 @@ -- Build files have been written to: /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu dh_auto_build - cd obj-i686-linux-gnu && make -j11 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j21 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/metabat-2.15 -B/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -732,23 +768,23 @@ make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' make -f src/CMakeFiles/metabat1.dir/build.make src/CMakeFiles/metabat1.dir/build +make -f src/CMakeFiles/contigOverlaps.dir/build.make src/CMakeFiles/contigOverlaps.dir/build make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' -make -f src/CMakeFiles/metabat2.dir/build.make src/CMakeFiles/metabat2.dir/build make -f src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/build.make src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/build +make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' +make -f src/CMakeFiles/metabat2.dir/build.make src/CMakeFiles/metabat2.dir/build make[3]: Entering directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' -make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' -make -f src/CMakeFiles/contigOverlaps.dir/build.make src/CMakeFiles/contigOverlaps.dir/build make[3]: Entering directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' -[ 12%] Building CXX object src/CMakeFiles/metabat2.dir/metabat2.cpp.o -[ 25%] Building CXX object src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o +[ 37%] Building CXX object src/CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o +[ 37%] Building CXX object src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o [ 37%] Building CXX object src/CMakeFiles/metabat1.dir/metabat1.cpp.o -cd /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -MD -MT src/CMakeFiles/metabat2.dir/metabat2.cpp.o -MF CMakeFiles/metabat2.dir/metabat2.cpp.o.d -o CMakeFiles/metabat2.dir/metabat2.cpp.o -c /build/reproducible-path/metabat-2.15/src/metabat2.cpp cd /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -MD -MT src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o -MF CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o.d -o CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o -c /build/reproducible-path/metabat-2.15/src/jgi_summarize_bam_contig_depths.cpp cd /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -MD -MT src/CMakeFiles/metabat1.dir/metabat1.cpp.o -MF CMakeFiles/metabat1.dir/metabat1.cpp.o.d -o CMakeFiles/metabat1.dir/metabat1.cpp.o -c /build/reproducible-path/metabat-2.15/src/metabat1.cpp -[ 50%] Building CXX object src/CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o cd /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -MD -MT src/CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o -MF CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o.d -o CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o -c /build/reproducible-path/metabat-2.15/src/contigOverlaps.cpp +[ 50%] Building CXX object src/CMakeFiles/metabat2.dir/metabat2.cpp.o +cd /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++11 -MD -MT src/CMakeFiles/metabat2.dir/metabat2.cpp.o -MF CMakeFiles/metabat2.dir/metabat2.cpp.o.d -o CMakeFiles/metabat2.dir/metabat2.cpp.o -c /build/reproducible-path/metabat-2.15/src/metabat2.cpp In file included from /usr/include/boost/math/policies/error_handling.hpp:11, from /usr/include/boost/math/distributions/detail/common_error_handling.hpp:12, from /usr/include/boost/math/distributions/arcsine.hpp:35, @@ -825,10 +861,10 @@ make[1]: Entering directory '/build/reproducible-path/metabat-2.15' cp -a test/contigs_depth.txt obj-i686-linux-gnu dh_auto_test - cd obj-i686-linux-gnu && make -j11 test ARGS\+=--verbose ARGS\+=-j11 + cd obj-i686-linux-gnu && make -j21 test ARGS\+=--verbose ARGS\+=-j21 make[2]: Entering directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j11 +/usr/bin/ctest --force-new-ctest-process --verbose -j21 UpdateCTestConfiguration from :/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu @@ -856,66 +892,66 @@ 3: Test command: /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/src/metabat2 "--inFile" "/build/reproducible-path/metabat-2.15/test/contigs.fa" "--abdFile" "/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/contigs_depth.txt" "--outFile" "/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/contigs_bins" "-v" 3: Working Directory: /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/test 3: Test timeout computed to be: 10000000 -2: MetaBAT 1 (nosha) using p1 90.0%, p2 90.0%, p3 95.0%, minProb 80.0%, minBinned 40%, minCV 1.0, minContig 2500, minContigByCorr 1000, minCorr 92%, paired 0, and 20 bootstrapping -3: MetaBAT 2 (nosha) using minContig 2500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=1713934052 -3: [00:00:00] Executing with 13 threads -3: [00:00:00] Parsing abundance file -3: [00:00:00] Parsing assembly file -3: [00:00:00] Number of large contigs >= 2500 are 1. -3: [00:00:00] Reading abundance file -3: [00:00:00] Finished reading 1 contigs and 1 coverages from /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/contigs_depth.txt -3: [00:00:00] Number of target contigs: 1 of large (>= 2500) and 0 of small ones (>=1000 & <2500). -2: [00:00:00] Finished reading 1 contigs. Number of target contigs >= 2500 are 1, and [1000 and 2500) are 0 -2: [00:00:00] Finished reading 1 contigs (using 1 including 0 short contigs) and 1 coverages from /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/contigs_depth.txt -2: [Info] Correlation binning won't be applied since the number of samples (1) < minSamples (10) 1: Reference fasta file /build/reproducible-path/metabat-2.15/test/contigs.fa 1: Output depth matrix to /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/contigs_depth.txt +2: MetaBAT 1 (nosha) using p1 90.0%, p2 90.0%, p3 95.0%, minProb 80.0%, minBinned 40%, minCV 1.0, minContig 2500, minContigByCorr 1000, minCorr 92%, paired 0, and 20 bootstrapping 1: jgi_summarize_bam_contig_depths nosha 1: Output matrix to /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/contigs_depth.txt 1: Reading reference fasta file: /build/reproducible-path/metabat-2.15/test/contigs.fa 1: ... 1 sequences +2: [00:00:00] Finished reading 1 contigs. Number of target contigs >= 2500 are 1, and [1000 and 2500) are 0 +2: [00:00:00] Finished reading 1 contigs (using 1 including 0 short contigs) and 1 coverages from /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/contigs_depth.txt +2: [Info] Correlation binning won't be applied since the number of samples (1) < minSamples (10) 1: 0: Opening bam: /build/reproducible-path/metabat-2.15/test/contigs-1000.fastq.bam +3: MetaBAT 2 (nosha) using minContig 2500, minCV 1.0, minCVSum 1.0, maxP 95%, minS 60, maxEdges 200 and minClsSize 200000. with random seed=1748344326 +3: [00:00:00] Executing with 24 threads +3: [00:00:00] Parsing abundance file +3: [00:00:00] Parsing assembly file +3: [00:00:00] Number of large contigs >= 2500 are 1. +3: [00:00:00] Reading abundance file +3: [00:00:00] Finished reading 1 contigs and 1 coverages from /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/contigs_depth.txt +3: [00:00:00] Number of target contigs: 1 of large (>= 2500) and 0 of small ones (>=1000 & <2500). 2: [00:00:00] Finished TNF calculation. -3: [00:00:00] Start TNF calculation. nobs = 1 -2: [00:00:00] Finished building a probabilistic graph. (1 vertices and 0 edges) -3: [00:00:00] Finished TNF calculation. 1: Processing bam files +2: [00:00:00] Finished building a probabilistic graph. (1 vertices and 0 edges) +3: [00:00:00] Start TNF calculation. nobs = 1 1: Thread 0 finished: contigs-1000.fastq.bam with 1000 reads and 1000 readsWellMapped 1: Creating depth matrix file: /build/reproducible-path/metabat-2.15/obj-i686-linux-gnu/contigs_depth.txt +3: [00:00:00] Finished TNF calculation. 1: Closing most bam files 1: Closing last bam file 1: Finished -1/3 Test #1: test_depths ...................... Passed 0.21 sec -2: [00:00:00] Bootstrapping 1/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 2/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 3/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 4/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 5/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 6/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 7/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 8/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 9/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 10/20 [-31.8Gb / 7.7Gb] [00:00:00] Bootstrapping 11/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 12/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 13/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 14/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 15/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 16/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 17/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 18/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 19/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 20/20 [-31.8Gb / 7.7Gb] [00:00:01] Bootstrapping 20/20 [-31.8Gb / 7.7Gb] +1/3 Test #1: test_depths ...................... Passed 0.10 sec +2: [00:00:00] Bootstrapping 1/20 [-29.3Gb / 7.7Gb] [00:00:00] Bootstrapping 2/20 [-29.3Gb / 7.7Gb] [00:00:00] Bootstrapping 3/20 [-29.3Gb / 7.7Gb] [00:00:00] Bootstrapping 4/20 [-29.4Gb / 7.7Gb] [00:00:00] Bootstrapping 5/20 [-29.4Gb / 7.7Gb] [00:00:00] Bootstrapping 6/20 [-29.4Gb / 7.7Gb] [00:00:00] Bootstrapping 7/20 [-29.3Gb / 7.7Gb] [00:00:00] Bootstrapping 8/20 [-29.3Gb / 7.7Gb] [00:00:00] Bootstrapping 9/20 [-29.4Gb / 7.7Gb] [00:00:00] Bootstrapping 10/20 [-29.5Gb / 7.7Gb] [00:00:00] Bootstrapping 11/20 [-29.5Gb / 7.7Gb] [00:00:00] Bootstrapping 12/20 [-29.5Gb / 7.7Gb] [00:00:00] Bootstrapping 13/20 [-29.5Gb / 7.7Gb] [00:00:00] Bootstrapping 14/20 [-29.5Gb / 7.7Gb] [00:00:00] Bootstrapping 15/20 [-29.4Gb / 7.7Gb] [00:00:00] Bootstrapping 16/20 [-29.6Gb / 7.7Gb] [00:00:00] Bootstrapping 17/20 [-29.6Gb / 7.7Gb] [00:00:00] Bootstrapping 18/20 [-29.6Gb / 7.7Gb] [00:00:00] Bootstrapping 19/20 [-29.6Gb / 7.7Gb] [00:00:01] Bootstrapping 20/20 [-29.6Gb / 7.7Gb] [00:00:01] Bootstrapping 20/20 [-29.6Gb / 7.7Gb] 2: [00:00:01] Saved bootstrap intermediate file (boot.514673552) for reuse in case of failure -2: [00:00:01] Building Ensemble Graph 0.0% (0 of 1), ETA -596523:-14:-8 [-31.8Gb / 7.7Gb] [00:00:01] Finished Ensemble Graph (1 vertices and 0 edges) [0.0Gb / 0.0Gb] -2: [00:00:01] Starting Ensemble Binning [-31.8Gb / 7.7Gb] -2: [00:00:01] Running Ensemble Binning [-31.8Gb / 7.7Gb] [00:00:01] Running Ensemble Binning 1 [-31.8Gb / 7.7Gb] [00:00:01] Running Ensemble Binning 1 [-31.8Gb / 7.7Gb] -2: [00:00:01] Finished Ensemble Binning [-31.8Gb / 7.7Gb] +2: [00:00:01] Building Ensemble Graph 0.0% (0 of 1), ETA -596523:-14:-8 [-29.6Gb / 7.7Gb] [00:00:01] Finished Ensemble Graph (1 vertices and -9223372036854775808 edges) [0.0Gb / 0.0Gb] +2: [00:00:01] Starting Ensemble Binning [-29.6Gb / 7.7Gb] +2: [00:00:01] Running Ensemble Binning [-29.6Gb / 7.7Gb] [00:00:01] Running Ensemble Binning 1 [-29.6Gb / 7.7Gb] [00:00:01] Running Ensemble Binning 1 [-29.6Gb / 7.7Gb] +2: [00:00:01] Finished Ensemble Binning [-29.6Gb / 7.7Gb] 2: [00:00:01] Cleaned up intermediate files 2: [00:00:01] 0.00% (0 out of 5404 bases) was binned. 2: Number of clusters formed: 0 -2/3 Test #2: test_metabat1 .................... Passed 1.68 sec -3: [00:00:00] Preparing TNF Graph Building [pTNF = 99.9; 0 / 1 (P = 0.00%) round 1] [00:00:00] Preparing TNF Graph Building [pTNF = 99.7; 0 / 1 (P = 0.00%) round 2] [00:00:00] Preparing TNF Graph Building [pTNF = 99.6; 0 / 1 (P = 0.00%) round 3] [00:00:00] Preparing TNF Graph Building [pTNF = 99.5; 0 / 1 (P = 0.00%) round 4] [00:00:00] Preparing TNF Graph Building [pTNF = 99.4; 0 / 1 (P = 0.00%) round 5] [00:00:00] Preparing TNF Graph Building [pTNF = 99.1; 0 / 1 (P = 0.00%) round 6] [00:00:00] Preparing TNF Graph Building [pTNF = 98.8; 0 / 1 (P = 0.00%) round 7] [00:00:00] Preparing TNF Graph Building [pTNF = 98.5; 0 / 1 (P = 0.00%) round 8] [00:00:00] Preparing TNF Graph Building [pTNF = 98.0; 0 / 1 (P = 0.00%) round 9] [00:00:00] Preparing TNF Graph Building [pTNF = 97.7; 0 / 1 (P = 0.00%) round 10] [00:00:00] Preparing TNF Graph Building [pTNF = 97.3; 0 / 1 (P = 0.00%) round 11] [00:00:00] Preparing TNF Graph Building [pTNF = 96.9; 0 / 1 (P = 0.00%) round 12] [00:00:00] Preparing TNF Graph Building [pTNF = 96.5; 0 / 1 (P = 0.00%) round 13] [00:00:00] Preparing TNF Graph Building [pTNF = 96.1; 0 / 1 (P = 0.00%) round 14] [00:00:00] Preparing TNF Graph Building [pTNF = 95.8; 0 / 1 (P = 0.00%) round 15] [00:00:00] Preparing TNF Graph Building [pTNF = 95.3; 0 / 1 (P = 0.00%) round 16] [00:00:00] Preparing TNF Graph Building [pTNF = 95.0; 0 / 1 (P = 0.00%) round 17] [00:00:00] Preparing TNF Graph Building [pTNF = 94.7; 0 / 1 (P = 0.00%) round 18] [00:00:00] Preparing TNF Graph Building [pTNF = 94.2; 0 / 1 (P = 0.00%) round 19] [00:00:00] Preparing TNF Graph Building [pTNF = 93.9; 0 / 1 (P = 0.00%) round 20] [00:00:01] Preparing TNF Graph Building [pTNF = 93.5; 0 / 1 (P = 0.00%) round 21] [00:00:01] Preparing TNF Graph Building [pTNF = 93.0; 0 / 1 (P = 0.00%) round 22] [00:00:01] Preparing TNF Graph Building [pTNF = 92.7; 0 / 1 (P = 0.00%) round 23] [00:00:01] Preparing TNF Graph Building [pTNF = 92.4; 0 / 1 (P = 0.00%) round 24] [00:00:01] Preparing TNF Graph Building [pTNF = 92.0; 0 / 1 (P = 0.00%) round 25] [00:00:01] Preparing TNF Graph Building [pTNF = 91.5; 0 / 1 (P = 0.00%) round 26] [00:00:01] Preparing TNF Graph Building [pTNF = 91.1; 0 / 1 (P = 0.00%) round 27] [00:00:01] Preparing TNF Graph Building [pTNF = 90.7; 0 / 1 (P = 0.00%) round 28] [00:00:01] Preparing TNF Graph Building [pTNF = 90.2; 0 / 1 (P = 0.00%) round 29] [00:00:01] Preparing TNF Graph Building [pTNF = 89.9; 0 / 1 (P = 0.00%) round 30] [00:00:01] Preparing TNF Graph Building [pTNF = 89.0; 0 / 1 (P = 0.00%) round 31] [00:00:01] Preparing TNF Graph Building [pTNF = 88.0; 0 / 1 (P = 0.00%) round 32] [00:00:01] Preparing TNF Graph Building [pTNF = 86.9; 0 / 1 (P = 0.00%) round 33] [00:00:01] Preparing TNF Graph Building [pTNF = 86.0; 0 / 1 (P = 0.00%) round 34] [00:00:01] Preparing TNF Graph Building [pTNF = 84.9; 0 / 1 (P = 0.00%) round 35] [00:00:01] Preparing TNF Graph Building [pTNF = 83.9; 0 / 1 (P = 0.00%) round 36] [00:00:01] Preparing TNF Graph Building [pTNF = 82.9; 0 / 1 (P = 0.00%) round 37] [00:00:01] Preparing TNF Graph Building [pTNF = 81.9; 0 / 1 (P = 0.00%) round 38] [00:00:01] Preparing TNF Graph Building [pTNF = 80.9; 0 / 1 (P = 0.00%) round 39] [00:00:01] Preparing TNF Graph Building [pTNF = 80.0; 0 / 1 (P = 0.00%) round 40] [00:00:01] Preparing TNF Graph Building [pTNF = 79.1; 0 / 1 (P = 0.00%) round 41] [00:00:01] Preparing TNF Graph Building [pTNF = 78.0; 0 / 1 (P = 0.00%) round 42] [00:00:01] Preparing TNF Graph Building [pTNF = 76.9; 0 / 1 (P = 0.00%) round 43] [00:00:01] Preparing TNF Graph Building [pTNF = 75.8; 0 / 1 (P = 0.00%) round 44] [00:00:02] Preparing TNF Graph Building [pTNF = 74.7; 0 / 1 (P = 0.00%) round 45] [00:00:02] Preparing TNF Graph Building [pTNF = 73.6; 0 / 1 (P = 0.00%) round 46] [00:00:02] Preparing TNF Graph Building [pTNF = 72.5; 0 / 1 (P = 0.00%) round 47] [00:00:02] Preparing TNF Graph Building [pTNF = 71.4; 0 / 1 (P = 0.00%) round 48] [00:00:02] Preparing TNF Graph Building [pTNF = 70.5; 0 / 1 (P = 0.00%) round 49] [00:00:02] Finished Preparing TNF Graph Building [pTNF = 69.40] -3: [00:00:02] Finished Building TNF Graph (0 edges) [-31.8Gb / 7.7Gb] +2/3 Test #2: test_metabat1 .................... Passed 1.07 sec +3: [00:00:00] Preparing TNF Graph Building [pTNF = 99.9; 0 / 1 (P = 0.00%) round 1] [00:00:00] Preparing TNF Graph Building [pTNF = 99.7; 0 / 1 (P = 0.00%) round 2] [00:00:00] Preparing TNF Graph Building [pTNF = 99.4; 0 / 1 (P = 0.00%) round 3] [00:00:00] Preparing TNF Graph Building [pTNF = 99.2; 0 / 1 (P = 0.00%) round 4] [00:00:00] Preparing TNF Graph Building [pTNF = 99.1; 0 / 1 (P = 0.00%) round 5] [00:00:00] Preparing TNF Graph Building [pTNF = 99.0; 0 / 1 (P = 0.00%) round 6] [00:00:00] Preparing TNF Graph Building [pTNF = 98.6; 0 / 1 (P = 0.00%) round 7] [00:00:00] Preparing TNF Graph Building [pTNF = 98.3; 0 / 1 (P = 0.00%) round 8] [00:00:00] Preparing TNF Graph Building [pTNF = 97.9; 0 / 1 (P = 0.00%) round 9] [00:00:00] Preparing TNF Graph Building [pTNF = 97.4; 0 / 1 (P = 0.00%) round 10] [00:00:00] Preparing TNF Graph Building [pTNF = 97.1; 0 / 1 (P = 0.00%) round 11] [00:00:00] Preparing TNF Graph Building [pTNF = 96.8; 0 / 1 (P = 0.00%) round 12] [00:00:00] Preparing TNF Graph Building [pTNF = 96.5; 0 / 1 (P = 0.00%) round 13] [00:00:00] Preparing TNF Graph Building [pTNF = 96.0; 0 / 1 (P = 0.00%) round 14] [00:00:00] Preparing TNF Graph Building [pTNF = 95.5; 0 / 1 (P = 0.00%) round 15] [00:00:00] Preparing TNF Graph Building [pTNF = 95.0; 0 / 1 (P = 0.00%) round 16] [00:00:00] Preparing TNF Graph Building [pTNF = 94.7; 0 / 1 (P = 0.00%) round 17] [00:00:00] Preparing TNF Graph Building [pTNF = 94.4; 0 / 1 (P = 0.00%) round 18] [00:00:00] Preparing TNF Graph Building [pTNF = 94.0; 0 / 1 (P = 0.00%) round 19] [00:00:00] Preparing TNF Graph Building [pTNF = 93.7; 0 / 1 (P = 0.00%) round 20] [00:00:00] Preparing TNF Graph Building [pTNF = 93.2; 0 / 1 (P = 0.00%) round 21] [00:00:00] Preparing TNF Graph Building [pTNF = 92.7; 0 / 1 (P = 0.00%) round 22] [00:00:00] Preparing TNF Graph Building [pTNF = 92.2; 0 / 1 (P = 0.00%) round 23] [00:00:00] Preparing TNF Graph Building [pTNF = 91.7; 0 / 1 (P = 0.00%) round 24] [00:00:00] Preparing TNF Graph Building [pTNF = 91.3; 0 / 1 (P = 0.00%) round 25] [00:00:00] Preparing TNF Graph Building [pTNF = 90.8; 0 / 1 (P = 0.00%) round 26] [00:00:00] Preparing TNF Graph Building [pTNF = 90.4; 0 / 1 (P = 0.00%) round 27] [00:00:00] Preparing TNF Graph Building [pTNF = 89.9; 0 / 1 (P = 0.00%) round 28] [00:00:01] Preparing TNF Graph Building [pTNF = 88.9; 0 / 1 (P = 0.00%) round 29] [00:00:01] Preparing TNF Graph Building [pTNF = 87.9; 0 / 1 (P = 0.00%) round 30] [00:00:01] Preparing TNF Graph Building [pTNF = 86.9; 0 / 1 (P = 0.00%) round 31] [00:00:01] Preparing TNF Graph Building [pTNF = 85.9; 0 / 1 (P = 0.00%) round 32] [00:00:01] Preparing TNF Graph Building [pTNF = 84.8; 0 / 1 (P = 0.00%) round 33] [00:00:01] Preparing TNF Graph Building [pTNF = 83.9; 0 / 1 (P = 0.00%) round 34] [00:00:01] Preparing TNF Graph Building [pTNF = 83.0; 0 / 1 (P = 0.00%) round 35] [00:00:01] Preparing TNF Graph Building [pTNF = 82.0; 0 / 1 (P = 0.00%) round 36] [00:00:01] Preparing TNF Graph Building [pTNF = 80.9; 0 / 1 (P = 0.00%) round 37] [00:00:01] Preparing TNF Graph Building [pTNF = 79.9; 0 / 1 (P = 0.00%) round 38] [00:00:01] Preparing TNF Graph Building [pTNF = 78.9; 0 / 1 (P = 0.00%) round 39] [00:00:01] Preparing TNF Graph Building [pTNF = 78.0; 0 / 1 (P = 0.00%) round 40] [00:00:01] Preparing TNF Graph Building [pTNF = 77.1; 0 / 1 (P = 0.00%) round 41] [00:00:01] Preparing TNF Graph Building [pTNF = 76.2; 0 / 1 (P = 0.00%) round 42] [00:00:01] Preparing TNF Graph Building [pTNF = 75.2; 0 / 1 (P = 0.00%) round 43] [00:00:01] Preparing TNF Graph Building [pTNF = 74.1; 0 / 1 (P = 0.00%) round 44] [00:00:01] Preparing TNF Graph Building [pTNF = 73.2; 0 / 1 (P = 0.00%) round 45] [00:00:01] Preparing TNF Graph Building [pTNF = 72.1; 0 / 1 (P = 0.00%) round 46] [00:00:01] Preparing TNF Graph Building [pTNF = 71.1; 0 / 1 (P = 0.00%) round 47] [00:00:01] Preparing TNF Graph Building [pTNF = 70.2; 0 / 1 (P = 0.00%) round 48] [00:00:01] Finished Preparing TNF Graph Building [pTNF = 69.30] +3: [00:00:01] Finished Building TNF Graph (0 edges) [-29.8Gb / 7.7Gb] 3: No edges were formed by TNF. -3: [00:00:02] Rescuing singleton large contigs -3: [00:00:02] There are 0 bins already -3: [00:00:02] Outputting bins -3: [00:00:02] -nan% (0 bases) of large (>=2500) and 0.00% (0 bases) of small (<2500) contigs were binned. +3: [00:00:01] Rescuing singleton large contigs +3: [00:00:01] There are 0 bins already +3: [00:00:01] Outputting bins +3: [00:00:01] -nan% (0 bases) of large (>=2500) and 0.00% (0 bases) of small (<2500) contigs were binned. 3: 0 bins (0 bases in total) formed. -3: [00:00:02] Finished -3/3 Test #3: test_metabat2 .................... Passed 2.20 sec +3: [00:00:01] Finished +3/3 Test #3: test_metabat2 .................... Passed 1.32 sec 100% tests passed, 0 tests failed out of 3 -Total Test time (real) = 2.22 sec +Total Test time (real) = 1.33 sec make[2]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/metabat-2.15' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/metabat/ - cd obj-i686-linux-gnu && make -j11 install DESTDIR=/build/reproducible-path/metabat-2.15/debian/metabat AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j21 install DESTDIR=/build/reproducible-path/metabat-2.15/debian/metabat AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/metabat-2.15 -B/build/reproducible-path/metabat-2.15/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -966,8 +1002,8 @@ dpkg-gencontrol: warning: package metabat: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb -dpkg-deb: building package 'metabat' in '../metabat_2.15-4_i386.deb'. dpkg-deb: building package 'metabat-dbgsym' in '../metabat-dbgsym_2.15-4_i386.deb'. +dpkg-deb: building package 'metabat' in '../metabat_2.15-4_i386.deb'. dpkg-genbuildinfo --build=binary -O../metabat_2.15-4_i386.buildinfo dpkg-genchanges --build=binary -O../metabat_2.15-4_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -975,12 +1011,14 @@ 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/3189/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3189/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/11826 and its subdirectories -I: Current time: Tue Apr 23 16:47:59 -12 2024 -I: pbuilder-time-stamp: 1713934079 +I: removing directory /srv/workspace/pbuilder/3189 and its subdirectories +I: Current time: Wed May 28 01:12:18 +14 2025 +I: pbuilder-time-stamp: 1748344338