Diff of the two buildlogs: -- --- b1/build.log 2024-04-15 07:27:38.367101387 +0000 +++ b2/build.log 2024-04-15 07:35:21.363367354 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Sun Apr 14 19:22:01 -12 2024 -I: pbuilder-time-stamp: 1713165721 +I: Current time: Mon Apr 15 21:27:50 +14 2024 +I: pbuilder-time-stamp: 1713166070 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying implicit-function.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/9756/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/31194/tmp/hooks/D01_modify_environment starting +debug: Running on ff4a. +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 Apr 15 07:28 /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/31194/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/31194/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='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='armhf' + 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]="arm-unknown-linux-gnueabihf") + 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=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='c81da4d05cb54872a4043a087d283b8b' - 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='9756' - PS1='# ' - PS2='> ' + INVOCATION_ID=ef7f38ea651940f9b1361540c8c7e128 + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + 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=31194 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.pY2sbww6/pbuilderrc_EIVB --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.pY2sbww6/b1 --logfile b1/build.log microbiomeutil_20101212+dfsg1-6.dsc' - SUDO_GID='110' - SUDO_UID='103' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + 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.pY2sbww6/pbuilderrc_GtQw --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.pY2sbww6/b2 --logfile b2/build.log microbiomeutil_20101212+dfsg1-6.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt64z 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 14 11:25 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/9756/tmp/hooks/D02_print_environment finished +I: user script /srv/workspace/pbuilder/31194/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -173,7 +205,7 @@ Get: 50 http://deb.debian.org/debian trixie/main armhf ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf ncbi-blast+ armhf 2.12.0+ds-4 [10.9 MB] Get: 52 http://deb.debian.org/debian trixie/main armhf ncbi-blast+-legacy all 2.12.0+ds-4 [8956 B] -Fetched 39.1 MB in 1s (45.8 MB/s) +Fetched 39.1 MB in 2s (17.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:armhf. (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 ... 19635 files and directories currently installed.) @@ -354,8 +386,8 @@ Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' -Local time is now: Mon Apr 15 07:23:01 UTC 2024. -Universal Time is now: Mon Apr 15 07:23:01 UTC 2024. +Local time is now: Mon Apr 15 07:28:48 UTC 2024. +Universal Time is now: Mon Apr 15 07:28:48 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up autotools-dev (20220109.1) ... @@ -404,7 +436,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/ && 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 > ../microbiomeutil_20101212+dfsg1-6_source.changes +I: user script /srv/workspace/pbuilder/31194/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/31194/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/microbiomeutil-20101212+dfsg1/ && 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 > ../microbiomeutil_20101212+dfsg1-6_source.changes dpkg-buildpackage: info: source package microbiomeutil dpkg-buildpackage: info: source version 20101212+dfsg1-6 dpkg-buildpackage: info: source distribution unstable @@ -416,7 +452,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_clean - make -j3 clean + make -j4 clean make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ @@ -469,7 +505,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_build - make -j3 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ @@ -500,13 +536,13 @@ formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2>/dev/null -Building a new DB, current time: 04/14/2024 19:23:16 +Building a new DB, current time: 04/15/2024 21:29:02 New DB name: /build/reproducible-path/microbiomeutil-20101212+dfsg1/RESOURCES/rRNA16S.gold.fasta New DB title: RESOURCES/rRNA16S.gold.fasta Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B -Adding sequences from FASTA; added 5181 sequences in 0.881838 seconds. +Adding sequences from FASTA; added 5181 sequences in 0.970699 seconds. cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta @@ -515,57 +551,51 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' dh_auto_test - make -j3 test + make -j4 test make[2]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1' cd NAST-iEr; make test cd WigeoN; make test cd ChimeraSlayer; make test +make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. -cd ./sample_data; make test +make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer' -make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' -# make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make test -make[3]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' -make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make test -#*************** TESTING NAST-iEr *********************** +cd ./sample_data; make test +make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' +# +make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' +# make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' # -#********** TESTING Chimera Slayer *************" -make[4]: Entering directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' +#************* TESTING WigeoN ********************" # +#********** TESTING Chimera Slayer *************" +#*************** TESTING NAST-iEr *********************** # # ./runMe.sh -#************* TESTING WigeoN ********************" +./runMe.sh ./testForUtils.pl -# ./runMe.sh + + +query to NAST format +../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST\n\n CMD: ../../ChimeraSlayer/ChimeraParentSelector/run_chimeraParentSelector.pl --query_NAST chims.NAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta --db_FASTA ../../RESOURCES/rRNA16S.gold.fasta -n 15 -P 90 -R 1.007 > chims.NAST.CPS Can't locate Fasta_reader.pm in @INC (you may need to install the Fasta_reader module) (@INC entries checked: /usr/lib/WigeoN/PerlLib /etc/perl /usr/local/lib/arm-linux-gnueabihf/perl/5.38.2 /usr/local/share/perl/5.38.2 /usr/lib/arm-linux-gnueabihf/perl5/5.38 /usr/share/perl5 /usr/lib/arm-linux-gnueabihf/perl-base /usr/lib/arm-linux-gnueabihf/perl/5.38 /usr/share/perl/5.38 /usr/local/lib/site_perl) at ../run_WigeoN.pl line 13. BEGIN failed--compilation aborted at ../run_WigeoN.pl line 13. -./runMe.sh make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' - - -query to NAST format -../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST - - make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/WigeoN' query and template (profile) to query NAST and template consensus NAST -../NAST-iEr -b template_seqs.NAST query_seq.fasta > tmp.both.NAST - - +../NAST-iEr -b template_seqs.NAST query_seq.fasta > tmp.both.NAST\n\n converting NAST mfasta to multi-alignment output highlighting differences -../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign - - +../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign\n\n Run via the megablast wrapper -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 Num template seqs to align to: 2 Alignment parameters: MATCH: 5 @@ -575,35 +605,35 @@ Highest score: 11681 make[4]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' make[3]: Leaving directory '/build/reproducible-path/microbiomeutil-20101212+dfsg1/NAST-iEr' - T(1)=2 s -ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 2 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 + T(1)=4 s +ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 4 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 + T(1)=4 s +ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 4 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 + T(1)=4 s +ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 4 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 T(1)=3 s -ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 3 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 - T(1)=2 s -ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 2 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 - T(1)=1 s -ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 +ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 3 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 1 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 - T(1)=2 s -ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 2 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 - T(1)=2 s -ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 2 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 - T(1)=2 s -ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 2 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 - T(1)=1 s -ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.13314.query --db_NAST /tmp/tmp.13314.db -R 1.007 +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 + T(1)=3 s +ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 3 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 + T(1)=3 s +ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 3 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 + T(1)=3 s +ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 3 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 T(1)=2 s -ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 2 seconds +ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 2 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.1342.query --db_NAST /tmp/tmp.1342.db -R 1.007 + T(1)=4 s +ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 4 seconds CMD: ../../ChimeraSlayer/ChimeraParentSelector/CPS_to_RENAST.pl --CPS_output chims.NAST.CPS --query_NAST chims.NAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta > chims.NAST.CPS_RENAST processing: ChimeraParentSelector chmraD24_7000004128191580_1-4580:4581-7682_S000428666 YES 100.00[(7000004128191580, NAST:164-4593, ECO:36-940, RawLen:876, G:90.90, L:100.00, 1.100);(S000428666, NAST:4594-6747, ECO:940-1470, RawLen:531, G:84.36, L:100.00, 1.185)] 10 entries from file chims.NAST were indexed in file chims.NAST.cidx @@ -678,42 +708,42 @@ Highest score: 11227 CMD: ../../ChimeraSlayer/ChimeraPhyloChecker/CPS_to_CPC.pl --CPS_output chims.NAST.CPS --query_NAST chims.NAST.CPS_RENAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta -P 90 -R 1.007 --minBS 90 --printAlignments > chims.NAST.CPS.CPC 10 entries from file chims.NAST.CPS_RENAST were indexed in file chims.NAST.CPS_RENAST.cidx -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (7000004128191580, S000428666) or (0, 1) took 7 seconds -ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 19 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000378387, S000016146) or (0, 1) took 9 seconds -ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 21 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (7000004131500344, S000127669) or (0, 1) took 7 seconds -ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 14 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000004801, S000437365) or (0, 1) took 8 seconds -ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 17 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000437007, S000437299) or (0, 1) took 6 seconds -ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 12 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000414109, S000253432) or (0, 1) took 6 seconds -ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 13 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (7000004131502379, 7000004128198963) or (0, 1) took 7 seconds -ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 21 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000503167, S000004272) or (0, 1) took 6 seconds -ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 9 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000436014, 7000004128189973) or (0, 1) took 6 seconds -ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 11 seconds -/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.18285.query --db_NAST /tmp/tmp.18285.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000009720, S000437236) or (0, 1) took 9 seconds -ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 21 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (7000004128191580, S000428666) or (0, 1) took 11 seconds +ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 34 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000378387, S000016146) or (0, 1) took 12 seconds +ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 28 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (7000004131500344, S000127669) or (0, 1) took 10 seconds +ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 20 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000004801, S000437365) or (0, 1) took 9 seconds +ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 22 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000437007, S000437299) or (0, 1) took 9 seconds +ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 18 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000414109, S000253432) or (0, 1) took 8 seconds +ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 21 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (7000004131502379, 7000004128198963) or (0, 1) took 11 seconds +ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 33 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000503167, S000004272) or (0, 1) took 9 seconds +ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 14 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000436014, 7000004128189973) or (0, 1) took 9 seconds +ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 15 seconds +/build/reproducible-path/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.3007.query --db_NAST /tmp/tmp.3007.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000009720, S000437236) or (0, 1) took 11 seconds +ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 26 seconds CMD: ../../ChimeraSlayer/util/CS_add_taxonomy.pl < chims.NAST.CPS.CPC > chims.NAST.CPS.CPC.wTaxons CMD: ../../ChimeraSlayer/ChimeraParentSelector/CPC_to_CPS.pl --CPC_output chims.NAST.CPS.CPC --query_NAST chims.NAST.CPS_RENAST --db_NAST ../../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta > chims.NAST.CPS.CPC.align - T(1)=1 s -ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds T(1)=0 s -ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds +ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 0 seconds + T(1)=1 s +ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 1 seconds T(1)=0 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 seconds T(1)=0 s @@ -724,8 +754,8 @@ ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 1 seconds T(1)=0 s ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 0 seconds - T(1)=1 s -ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 1 seconds + T(1)=0 s +ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 0 seconds T(1)=1 s @@ -799,8 +829,8 @@ dpkg-gencontrol: warning: package nast-ier: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package microbiomeutil-data: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package nast-ier: substitution variable ${perl:Depends} unused, but is defined -dpkg-gencontrol: warning: package wigeon: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package chimeraslayer: substitution variable ${perl:Depends} unused, but is defined +dpkg-gencontrol: warning: package wigeon: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-6_all.deb'. @@ -816,12 +846,14 @@ 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/31194/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/31194/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/9756 and its subdirectories -I: Current time: Sun Apr 14 19:27:34 -12 2024 -I: pbuilder-time-stamp: 1713166054 +I: removing directory /srv/workspace/pbuilder/31194 and its subdirectories +I: Current time: Mon Apr 15 21:35:17 +14 2024 +I: pbuilder-time-stamp: 1713166517