Diff of the two buildlogs: -- --- b1/build.log 2024-05-13 23:53:53.233738013 +0000 +++ b2/build.log 2024-05-13 23:56:00.236336526 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon May 13 11:51:47 -12 2024 -I: pbuilder-time-stamp: 1715644307 +I: Current time: Mon Jun 16 20:16:56 +14 2025 +I: pbuilder-time-stamp: 1750054616 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -28,51 +28,83 @@ 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/2460067/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1667311/tmp/hooks/D01_modify_environment starting +debug: Running on infom02-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Jun 16 06:17 /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/1667311/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1667311/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='d739a4395f48408fbaf3db74f46c8478' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='2460067' - PS1='# ' - PS2='> ' + INVOCATION_ID=7fb96c5b39ee4176ac07913b3bc34eb1 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=1667311 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.FRDtiYXy/pbuilderrc_n5vE --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.FRDtiYXy/b1 --logfile b1/build.log metabat_2.15-4.dsc' - SUDO_GID='109' - 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.FRDtiYXy/pbuilderrc_QsVh --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.FRDtiYXy/b2 --logfile b2/build.log metabat_2.15-4.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom01-amd64 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.6.13+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.6.13-1~bpo12+1 (2024-02-15) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 May 11 11:26 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2460067/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Jun 16 03:14 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1667311/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -235,7 +267,7 @@ Get: 103 http://deb.debian.org/debian trixie/main amd64 pkgconf-bin amd64 1.8.1-1+b2 [29.7 kB] Get: 104 http://deb.debian.org/debian trixie/main amd64 pkgconf amd64 1.8.1-1+b2 [26.2 kB] Get: 105 http://deb.debian.org/debian trixie/main amd64 pkg-config amd64 1.8.1-1+b2 [14.0 kB] -Fetched 72.8 MB in 1s (64.5 MB/s) +Fetched 72.8 MB in 1s (56.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) @@ -594,8 +626,8 @@ Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon May 13 23:53:08 UTC 2024. -Universal Time is now: Mon May 13 23:53:08 UTC 2024. +Local time is now: Mon Jun 16 06:18:13 UTC 2025. +Universal Time is now: Mon Jun 16 06:18:13 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:amd64 (1.83.0-2.1+b1) ... @@ -682,7 +714,11 @@ 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/1667311/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/1667311/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 @@ -763,28 +799,28 @@ make -f src/CMakeFiles/metabat1.dir/build.make src/CMakeFiles/metabat1.dir/build make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' -make -f src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/build.make src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/build +make -f src/CMakeFiles/metabat2.dir/build.make src/CMakeFiles/metabat2.dir/build make -f src/CMakeFiles/contigOverlaps.dir/build.make src/CMakeFiles/contigOverlaps.dir/build -make[3]: Entering directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-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]: Entering directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' -[ 25%] Building CXX object src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o -[ 25%] Building CXX object src/CMakeFiles/metabat1.dir/metabat1.cpp.o -cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +make[3]: Entering directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' +[ 12%] Building CXX object src/CMakeFiles/metabat1.dir/metabat1.cpp.o +[ 25%] Building CXX object src/CMakeFiles/metabat2.dir/metabat2.cpp.o cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 -[ 37%] Building CXX object src/CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o -cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 37%] Building CXX object src/CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o +cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 +[ 50%] Building CXX object src/CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o +cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/c++ -D_XOPEN_SOURCE=700 -I/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu -I/build/reproducible-path/metabat-2.15 -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 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, from /usr/include/boost/math/distributions.hpp:15, - from /build/reproducible-path/metabat-2.15/src/metabat1.h:40, - from /build/reproducible-path/metabat-2.15/src/metabat1.cpp:1: + from /build/reproducible-path/metabat-2.15/src/metabat2.h:45, + from /build/reproducible-path/metabat-2.15/src/metabat2.cpp:1: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ @@ -792,8 +828,8 @@ from /usr/include/boost/math/distributions/detail/common_error_handling.hpp:12, from /usr/include/boost/math/distributions/arcsine.hpp:35, from /usr/include/boost/math/distributions.hpp:15, - from /build/reproducible-path/metabat-2.15/src/metabat2.h:45, - from /build/reproducible-path/metabat-2.15/src/metabat2.cpp:1: + from /build/reproducible-path/metabat-2.15/src/metabat1.h:40, + from /build/reproducible-path/metabat-2.15/src/metabat1.cpp:1: /usr/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp] 23 | # warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" | ^~~~~~~ @@ -811,9 +847,6 @@ /build/reproducible-path/metabat-2.15/src/BamUtils.h:582:34: warning: ignoring return value of ‘bam1_t* bam_copy1(bam1_t*, const bam1_t*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 582 | bam_copy1(data->mate, orphan); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -[ 62%] Linking CXX executable contigOverlaps -cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/contigOverlaps.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o -o contigOverlaps -lhts /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libboost_program_options.a /usr/lib/x86_64-linux-gnu/libboost_filesystem.a /usr/lib/x86_64-linux-gnu/libboost_system.a /usr/lib/x86_64-linux-gnu/libboost_graph.a /usr/lib/x86_64-linux-gnu/libboost_serialization.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.a /usr/lib/x86_64-linux-gnu/libboost_regex.a /build/reproducible-path/metabat-2.15/src/metabat1.h:207:55: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 207 | template struct pair_equal_to: std::binary_function, bool> { | ^~~~~~~~~~~~~~~ @@ -823,8 +856,6 @@ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ -make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' -[ 62%] Built target contigOverlaps /build/reproducible-path/metabat-2.15/src/metabat1.cpp: In function ‘void pam_loop(int, ContigVector&, std::vector&, ContigSet&, ClassMap&)’: /build/reproducible-path/metabat-2.15/src/metabat1.cpp:1463:85: warning: ‘std::binder1st<_Operation> std::bind1st(const _Operation&, const _Tp&) [with _Operation = pair_equal_to; _Tp = int]’ is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] 1463 | medoid_vals[i] = std::find_if(rABD.begin(), rABD.end(), std::bind1st(pair_equal_to(),medoid_ids[i]))->second; @@ -833,6 +864,11 @@ /usr/include/c++/13/backward/binders.h:136:5: note: declared here 136 | bind1st(const _Operation& __fn, const _Tp& __x) | ^~~~~~~ +[ 62%] Linking CXX executable contigOverlaps +cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/contigOverlaps.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/contigOverlaps.dir/contigOverlaps.cpp.o -o contigOverlaps -lhts /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libboost_program_options.a /usr/lib/x86_64-linux-gnu/libboost_filesystem.a /usr/lib/x86_64-linux-gnu/libboost_system.a /usr/lib/x86_64-linux-gnu/libboost_graph.a /usr/lib/x86_64-linux-gnu/libboost_serialization.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.a /usr/lib/x86_64-linux-gnu/libboost_regex.a +make[3]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' +[ 62%] Built target contigOverlaps [ 75%] Linking CXX executable jgi_summarize_bam_contig_depths cd /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/jgi_summarize_bam_contig_depths.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/metabat-2.15=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -Wl,-z,relro -Wl,-z,now CMakeFiles/jgi_summarize_bam_contig_depths.dir/jgi_summarize_bam_contig_depths.cpp.o -o jgi_summarize_bam_contig_depths -lhts /usr/lib/x86_64-linux-gnu/libz.so /usr/lib/x86_64-linux-gnu/libboost_program_options.a /usr/lib/x86_64-linux-gnu/libboost_filesystem.a /usr/lib/x86_64-linux-gnu/libboost_system.a /usr/lib/x86_64-linux-gnu/libboost_graph.a /usr/lib/x86_64-linux-gnu/libboost_serialization.a /usr/lib/x86_64-linux-gnu/libboost_iostreams.a /usr/lib/x86_64-linux-gnu/libboost_regex.a @@ -892,11 +928,12 @@ 1: Output matrix to /build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu/contigs_depth.txt 1: Reading reference fasta file: /build/reproducible-path/metabat-2.15/test/contigs.fa 1: ... 1 sequences +1: 0: Opening bam: /build/reproducible-path/metabat-2.15/test/contigs-1000.fastq.bam 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 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-x86_64-linux-gnu/contigs_depth.txt 2: [Info] Correlation binning won't be applied since the number of samples (1) < minSamples (10) -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=1715644420 +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=1750054726 3: [00:00:00] Executing with 12 threads 3: [00:00:00] Parsing abundance file 3: [00:00:00] Parsing assembly file @@ -904,30 +941,29 @@ 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-x86_64-linux-gnu/contigs_depth.txt 3: [00:00:00] Number of target contigs: 1 of large (>= 2500) and 0 of small ones (>=1000 & <2500). -1: 0: Opening bam: /build/reproducible-path/metabat-2.15/test/contigs-1000.fastq.bam 2: [00:00:00] Finished TNF calculation. +3: [00:00:00] Start TNF calculation. nobs = 1 1: Processing bam files +2: [00:00:00] Finished building a probabilistic graph. (1 vertices and 0 edges) +3: [00:00:00] Finished TNF calculation. 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-x86_64-linux-gnu/contigs_depth.txt 1: Closing most bam files 1: Closing last bam file 1: Finished -2: [00:00:00] Finished building a probabilistic graph. (1 vertices and 0 edges) -3: [00:00:00] Start TNF calculation. nobs = 1 -1/3 Test #1: test_depths ...................... Passed 0.07 sec -3: [00:00:00] Calculating TNF 100.0% (1 of 1), ETA 0:00:00 [00:00:00] Finished TNF calculation. -2: [00:00:00] Bootstrapping 1/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 2/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 3/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 4/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 5/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 6/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 7/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 8/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 9/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 10/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 11/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 12/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 13/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 14/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 15/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 16/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 17/20 [-14.0Gb / 23.5Gb] [00:00:00] Bootstrapping 18/20 [-14.0Gb / 23.5Gb] [00:00:01] Bootstrapping 19/20 [-14.0Gb / 23.5Gb] [00:00:01] Bootstrapping 20/20 [-14.0Gb / 23.5Gb] [00:00:01] Bootstrapping 20/20 [-14.0Gb / 23.5Gb] +1/3 Test #1: test_depths ...................... Passed 0.10 sec +2: [00:00:00] Bootstrapping 1/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 2/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 3/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 4/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 5/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 6/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 7/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 8/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 9/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 10/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 11/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 12/20 [-22.4Gb / 23.5Gb] [00:00:00] Bootstrapping 13/20 [-22.3Gb / 23.5Gb] [00:00:00] Bootstrapping 14/20 [-22.3Gb / 23.5Gb] [00:00:00] Bootstrapping 15/20 [-22.3Gb / 23.5Gb] [00:00:01] Bootstrapping 16/20 [-22.3Gb / 23.5Gb] [00:00:01] Bootstrapping 17/20 [-22.3Gb / 23.5Gb] [00:00:01] Bootstrapping 18/20 [-22.3Gb / 23.5Gb] [00:00:01] Bootstrapping 19/20 [-22.3Gb / 23.5Gb] [00:00:01] Bootstrapping 20/20 [-22.3Gb / 23.5Gb] [00:00:01] Bootstrapping 20/20 [-22.3Gb / 23.5Gb] 2: [00:00:01] Saved bootstrap intermediate file (boot.6018994539096241237) for reuse in case of failure -2: [00:00:01] Building Ensemble Graph 0.0% (0 of 1), ETA -2562047788015215:-30:-8 [-14.0Gb / 23.5Gb] [00:00:01] Finished Ensemble Graph (1 vertices and 0 edges) [-14.0Gb / 23.5Gb] -2: [00:00:01] Starting Ensemble Binning [-14.0Gb / 23.5Gb] -2: [00:00:01] Running Ensemble Binning [-14.0Gb / 23.5Gb] [00:00:01] Running Ensemble Binning 1 [-14.0Gb / 23.5Gb] [00:00:01] Running Ensemble Binning 1 [-14.0Gb / 23.5Gb] -2: [00:00:01] Finished Ensemble Binning [-14.0Gb / 23.5Gb] +2: [00:00:01] Building Ensemble Graph 0.0% (0 of 1), ETA -2562047788015215:-30:-8 [-22.3Gb / 23.5Gb] [00:00:01] Finished Ensemble Graph (1 vertices and 0 edges) [-22.3Gb / 23.5Gb] +2: [00:00:01] Starting Ensemble Binning [-22.3Gb / 23.5Gb] +2: [00:00:01] Running Ensemble Binning [-22.3Gb / 23.5Gb] [00:00:01] Running Ensemble Binning 1 [-22.3Gb / 23.5Gb] [00:00:01] Running Ensemble Binning 1 [-22.3Gb / 23.5Gb] +2: [00:00:01] Finished Ensemble Binning [-22.3Gb / 23.5Gb] 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 1.13 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 = 99.8; 0 / 1 (P = 0.00%) round 2] [00:00:00] Preparing TNF Graph Building [pTNF = 99.5; 0 / 1 (P = 0.00%) round 3] [00:00:00] Preparing TNF Graph Building [pTNF = 99.3; 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 = 98.9; 0 / 1 (P = 0.00%) round 6] [00:00:00] Preparing TNF Graph Building [pTNF = 98.5; 0 / 1 (P = 0.00%) round 7] [00:00:00] Preparing TNF Graph Building [pTNF = 98.0; 0 / 1 (P = 0.00%) round 8] [00:00:00] Preparing TNF Graph Building [pTNF = 97.6; 0 / 1 (P = 0.00%) round 9] [00:00:00] Preparing TNF Graph Building [pTNF = 97.1; 0 / 1 (P = 0.00%) round 10] [00:00:00] Preparing TNF Graph Building [pTNF = 96.6; 0 / 1 (P = 0.00%) round 11] [00:00:00] Preparing TNF Graph Building [pTNF = 96.1; 0 / 1 (P = 0.00%) round 12] [00:00:00] Preparing TNF Graph Building [pTNF = 95.6; 0 / 1 (P = 0.00%) round 13] [00:00:00] Preparing TNF Graph Building [pTNF = 95.2; 0 / 1 (P = 0.00%) round 14] [00:00:00] Preparing TNF Graph Building [pTNF = 94.8; 0 / 1 (P = 0.00%) round 15] [00:00:00] Preparing TNF Graph Building [pTNF = 94.5; 0 / 1 (P = 0.00%) round 16] [00:00:00] Preparing TNF Graph Building [pTNF = 94.2; 0 / 1 (P = 0.00%) round 17] [00:00:00] Preparing TNF Graph Building [pTNF = 93.7; 0 / 1 (P = 0.00%) round 18] [00:00:00] Preparing TNF Graph Building [pTNF = 93.2; 0 / 1 (P = 0.00%) round 19] [00:00:00] Preparing TNF Graph Building [pTNF = 92.7; 0 / 1 (P = 0.00%) round 20] [00:00:00] Preparing TNF Graph Building [pTNF = 92.3; 0 / 1 (P = 0.00%) round 21] [00:00:00] Preparing TNF Graph Building [pTNF = 91.9; 0 / 1 (P = 0.00%) round 22] [00:00:00] Preparing TNF Graph Building [pTNF = 91.4; 0 / 1 (P = 0.00%) round 23] [00:00:00] Preparing TNF Graph Building [pTNF = 91.1; 0 / 1 (P = 0.00%) round 24] [00:00:00] Preparing TNF Graph Building [pTNF = 90.6; 0 / 1 (P = 0.00%) round 25] [00:00:00] Preparing TNF Graph Building [pTNF = 90.1; 0 / 1 (P = 0.00%) round 26] [00:00:00] Preparing TNF Graph Building [pTNF = 89.6; 0 / 1 (P = 0.00%) round 27] [00:00:00] Preparing TNF Graph Building [pTNF = 88.7; 0 / 1 (P = 0.00%) round 28] [00:00:01] Preparing TNF Graph Building [pTNF = 87.6; 0 / 1 (P = 0.00%) round 29] [00:00:01] Preparing TNF Graph Building [pTNF = 86.6; 0 / 1 (P = 0.00%) round 30] [00:00:01] Preparing TNF Graph Building [pTNF = 85.5; 0 / 1 (P = 0.00%) round 31] [00:00:01] Preparing TNF Graph Building [pTNF = 84.6; 0 / 1 (P = 0.00%) round 32] [00:00:01] Preparing TNF Graph Building [pTNF = 83.5; 0 / 1 (P = 0.00%) round 33] [00:00:01] Preparing TNF Graph Building [pTNF = 82.4; 0 / 1 (P = 0.00%) round 34] [00:00:01] Preparing TNF Graph Building [pTNF = 81.3; 0 / 1 (P = 0.00%) round 35] [00:00:01] Preparing TNF Graph Building [pTNF = 80.4; 0 / 1 (P = 0.00%) round 36] [00:00:01] Preparing TNF Graph Building [pTNF = 79.3; 0 / 1 (P = 0.00%) round 37] [00:00:01] Preparing TNF Graph Building [pTNF = 78.3; 0 / 1 (P = 0.00%) round 38] [00:00:01] Preparing TNF Graph Building [pTNF = 77.4; 0 / 1 (P = 0.00%) round 39] [00:00:01] Preparing TNF Graph Building [pTNF = 76.5; 0 / 1 (P = 0.00%) round 40] [00:00:01] Preparing TNF Graph Building [pTNF = 75.6; 0 / 1 (P = 0.00%) round 41] [00:00:01] Preparing TNF Graph Building [pTNF = 74.5; 0 / 1 (P = 0.00%) round 42] [00:00:01] Preparing TNF Graph Building [pTNF = 73.6; 0 / 1 (P = 0.00%) round 43] [00:00:01] Preparing TNF Graph Building [pTNF = 72.7; 0 / 1 (P = 0.00%) round 44] [00:00:01] Preparing TNF Graph Building [pTNF = 71.7; 0 / 1 (P = 0.00%) round 45] [00:00:01] Preparing TNF Graph Building [pTNF = 70.6; 0 / 1 (P = 0.00%) round 46] [00:00:01] Finished Preparing TNF Graph Building [pTNF = 69.50] -3: [00:00:01] Building TNF Graph 8900.0% (89 of 1), ETA 0:00:00 [-14.0Gb / 23.5Gb] [00:00:01] Finished Building TNF Graph (0 edges) [-14.0Gb / 23.5Gb] +2/3 Test #2: test_metabat1 .................... Passed 1.24 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 = 99.6; 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 = 99.1; 0 / 1 (P = 0.00%) round 4] [00:00:00] Preparing TNF Graph Building [pTNF = 99.0; 0 / 1 (P = 0.00%) round 5] [00:00:00] Preparing TNF Graph Building [pTNF = 98.6; 0 / 1 (P = 0.00%) round 6] [00:00:00] Preparing TNF Graph Building [pTNF = 98.3; 0 / 1 (P = 0.00%) round 7] [00:00:00] Preparing TNF Graph Building [pTNF = 98.0; 0 / 1 (P = 0.00%) round 8] [00:00:00] Preparing TNF Graph Building [pTNF = 97.5; 0 / 1 (P = 0.00%) round 9] [00:00:00] Preparing TNF Graph Building [pTNF = 97.0; 0 / 1 (P = 0.00%) round 10] [00:00:00] Preparing TNF Graph Building [pTNF = 96.7; 0 / 1 (P = 0.00%) round 11] [00:00:00] Preparing TNF Graph Building [pTNF = 96.4; 0 / 1 (P = 0.00%) round 12] [00:00:00] Preparing TNF Graph Building [pTNF = 96.1; 0 / 1 (P = 0.00%) round 13] [00:00:00] Preparing TNF Graph Building [pTNF = 95.8; 0 / 1 (P = 0.00%) round 14] [00:00:00] Preparing TNF Graph Building [pTNF = 95.3; 0 / 1 (P = 0.00%) round 15] [00:00:00] Preparing TNF Graph Building [pTNF = 94.9; 0 / 1 (P = 0.00%) round 16] [00:00:00] Preparing TNF Graph Building [pTNF = 94.5; 0 / 1 (P = 0.00%) round 17] [00:00:00] Preparing TNF Graph Building [pTNF = 94.1; 0 / 1 (P = 0.00%) round 18] [00:00:00] Preparing TNF Graph Building [pTNF = 93.8; 0 / 1 (P = 0.00%) round 19] [00:00:00] Preparing TNF Graph Building [pTNF = 93.3; 0 / 1 (P = 0.00%) round 20] [00:00:00] Preparing TNF Graph Building [pTNF = 92.9; 0 / 1 (P = 0.00%) round 21] [00:00:00] Preparing TNF Graph Building [pTNF = 92.6; 0 / 1 (P = 0.00%) round 22] [00:00:00] Preparing TNF Graph Building [pTNF = 92.1; 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 = 91.4; 0 / 1 (P = 0.00%) round 25] [00:00:00] Preparing TNF Graph Building [pTNF = 91.1; 0 / 1 (P = 0.00%) round 26] [00:00:00] Preparing TNF Graph Building [pTNF = 90.8; 0 / 1 (P = 0.00%) round 27] [00:00:01] Preparing TNF Graph Building [pTNF = 90.4; 0 / 1 (P = 0.00%) round 28] [00:00:01] Preparing TNF Graph Building [pTNF = 89.9; 0 / 1 (P = 0.00%) round 29] [00:00:01] Preparing TNF Graph Building [pTNF = 88.9; 0 / 1 (P = 0.00%) round 30] [00:00:01] Preparing TNF Graph Building [pTNF = 88.0; 0 / 1 (P = 0.00%) round 31] [00:00:01] Preparing TNF Graph Building [pTNF = 86.9; 0 / 1 (P = 0.00%) round 32] [00:00:01] Preparing TNF Graph Building [pTNF = 85.9; 0 / 1 (P = 0.00%) round 33] [00:00:01] Preparing TNF Graph Building [pTNF = 85.0; 0 / 1 (P = 0.00%) round 34] [00:00:01] Preparing TNF Graph Building [pTNF = 83.9; 0 / 1 (P = 0.00%) round 35] [00:00:01] Preparing TNF Graph Building [pTNF = 82.8; 0 / 1 (P = 0.00%) round 36] [00:00:01] Preparing TNF Graph Building [pTNF = 81.8; 0 / 1 (P = 0.00%) round 37] [00:00:01] Preparing TNF Graph Building [pTNF = 80.7; 0 / 1 (P = 0.00%) round 38] [00:00:01] Preparing TNF Graph Building [pTNF = 79.8; 0 / 1 (P = 0.00%) round 39] [00:00:01] Preparing TNF Graph Building [pTNF = 78.8; 0 / 1 (P = 0.00%) round 40] [00:00:01] Preparing TNF Graph Building [pTNF = 77.7; 0 / 1 (P = 0.00%) round 41] [00:00:01] Preparing TNF Graph Building [pTNF = 76.8; 0 / 1 (P = 0.00%) round 42] [00:00:01] Preparing TNF Graph Building [pTNF = 75.7; 0 / 1 (P = 0.00%) round 43] [00:00:01] Preparing TNF Graph Building [pTNF = 74.8; 0 / 1 (P = 0.00%) round 44] [00:00:01] Preparing TNF Graph Building [pTNF = 73.7; 0 / 1 (P = 0.00%) round 45] [00:00:01] Preparing TNF Graph Building [pTNF = 72.6; 0 / 1 (P = 0.00%) round 46] [00:00:01] Preparing TNF Graph Building [pTNF = 71.5; 0 / 1 (P = 0.00%) round 47] [00:00:01] Preparing TNF Graph Building [pTNF = 70.5; 0 / 1 (P = 0.00%) round 48] [00:00:01] Finished Preparing TNF Graph Building [pTNF = 69.60] +3: [00:00:01] Finished Building TNF Graph (0 edges) [-22.3Gb / 23.5Gb] 3: No edges were formed by TNF. 3: [00:00:01] Rescuing singleton large contigs 3: [00:00:01] There are 0 bins already @@ -935,11 +971,11 @@ 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: [00:00:01] Finished -3/3 Test #3: test_metabat2 .................... Passed 1.38 sec +3/3 Test #3: test_metabat2 .................... Passed 1.31 sec 100% tests passed, 0 tests failed out of 3 -Total Test time (real) = 1.38 sec +Total Test time (real) = 1.31 sec make[2]: Leaving directory '/build/reproducible-path/metabat-2.15/obj-x86_64-linux-gnu' make[1]: Leaving directory '/build/reproducible-path/metabat-2.15' create-stamp debian/debhelper-build-stamp @@ -1005,12 +1041,14 @@ 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/1667311/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1667311/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/2460067 and its subdirectories -I: Current time: Mon May 13 11:53:52 -12 2024 -I: pbuilder-time-stamp: 1715644432 +I: removing directory /srv/workspace/pbuilder/1667311 and its subdirectories +I: Current time: Mon Jun 16 20:18:59 +14 2025 +I: pbuilder-time-stamp: 1750054739