Diff of the two buildlogs: -- --- b1/build.log 2021-07-15 23:55:31.957733401 +0000 +++ b2/build.log 2021-07-16 00:02:06.446958424 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 15 11:42:07 -12 2021 -I: pbuilder-time-stamp: 1626392527 +I: Current time: Fri Jul 16 13:55:50 +14 2021 +I: pbuilder-time-stamp: 1626393350 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz] I: copying local configuration @@ -16,8 +16,8 @@ I: copying [./microbiomeutil_20101212+dfsg1-4.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' -gpgv: keyblock resource '/tmp/dpkg-verify-sig.NuU5I0cC/trustedkeys.kbx': General error -gpgv: Signature made Thu Jan 7 20:30:59 2021 -12 +gpgv: keyblock resource '/tmp/dpkg-verify-sig.9FSadbrg/trustedkeys.kbx': General error +gpgv: Signature made Fri Jan 8 22:30:59 2021 +14 gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1 gpgv: issuer "npatra974@gmail.com" gpgv: Can't check signature: No public key @@ -33,135 +33,169 @@ dpkg-source: info: applying enable_tests_in_local_dir.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/22929/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2929/tmp/hooks/D01_modify_environment starting +debug: Running on virt32b. +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 +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by 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/2929/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2929/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - 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,-fixfilepath parallel=5' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.1.4(1)-release' + BUILDDIR=/build + 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,-fixfilepath parallel=4' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='2b3b291dc6a44d28860e77e7d179cf2d' - 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='22929' - PS1='# ' - PS2='> ' + INVOCATION_ID=6f94a500afac4949a58e30d88ac90119 + 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=2929 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/tmp.0QkcFzxl8y/pbuilderrc_5ION --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0QkcFzxl8y/b1 --logfile b1/build.log microbiomeutil_20101212+dfsg1-4.dsc' - SUDO_GID='114' - SUDO_UID='109' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:8000/' + 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/tmp.0QkcFzxl8y/pbuilderrc_lt1z --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.0QkcFzxl8y/b2 --logfile b2/build.log --extrapackages usrmerge microbiomeutil_20101212+dfsg1-4.dsc' + SUDO_GID=112 + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:8000/ I: uname -a - Linux ff64a 5.10.0-7-arm64 #1 SMP Debian 5.10.40-1 (2021-05-28) aarch64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-7-armmp-lpae #1 SMP Debian 5.10.40-1 (2021-05-28) armv7l GNU/Linux I: ls -l /bin total 3580 - -rwxr-xr-x 1 root root 816764 Jun 21 14:26 bash - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bunzip2 - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzcat - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2225 Jul 20 2020 bzdiff - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Sep 4 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3775 Jul 20 2020 bzgrep - -rwxr-xr-x 3 root root 26052 Jul 20 2020 bzip2 - -rwxr-xr-x 1 root root 9636 Jul 20 2020 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 20 2020 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 20 2020 bzmore - -rwxr-xr-x 1 root root 26668 Sep 22 2020 cat - -rwxr-xr-x 1 root root 43104 Sep 22 2020 chgrp - -rwxr-xr-x 1 root root 38984 Sep 22 2020 chmod - -rwxr-xr-x 1 root root 43112 Sep 22 2020 chown - -rwxr-xr-x 1 root root 92616 Sep 22 2020 cp - -rwxr-xr-x 1 root root 75524 Dec 10 2020 dash - -rwxr-xr-x 1 root root 75880 Sep 22 2020 date - -rwxr-xr-x 1 root root 55436 Sep 22 2020 dd - -rwxr-xr-x 1 root root 59912 Sep 22 2020 df - -rwxr-xr-x 1 root root 96764 Sep 22 2020 dir - -rwxr-xr-x 1 root root 55012 Feb 7 02:38 dmesg - lrwxrwxrwx 1 root root 8 Nov 6 2019 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Nov 6 2019 domainname -> hostname - -rwxr-xr-x 1 root root 22508 Sep 22 2020 echo - -rwxr-xr-x 1 root root 28 Nov 9 2020 egrep - -rwxr-xr-x 1 root root 22496 Sep 22 2020 false - -rwxr-xr-x 1 root root 28 Nov 9 2020 fgrep - -rwxr-xr-x 1 root root 47492 Feb 7 02:38 findmnt - -rwsr-xr-x 1 root root 26076 Feb 26 04:12 fusermount - -rwxr-xr-x 1 root root 124508 Nov 9 2020 grep - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 gunzip - -rwxr-xr-x 1 root root 6376 Mar 2 11:30 gzexe - -rwxr-xr-x 1 root root 64212 Mar 2 11:30 gzip - -rwxr-xr-x 1 root root 13784 Nov 6 2019 hostname - -rwxr-xr-x 1 root root 43180 Sep 22 2020 ln - -rwxr-xr-x 1 root root 35068 Feb 7 2020 login - -rwxr-xr-x 1 root root 96764 Sep 22 2020 ls - -rwxr-xr-x 1 root root 99940 Feb 7 02:38 lsblk - -rwxr-xr-x 1 root root 51408 Sep 22 2020 mkdir - -rwxr-xr-x 1 root root 43184 Sep 22 2020 mknod - -rwxr-xr-x 1 root root 30780 Sep 22 2020 mktemp - -rwxr-xr-x 1 root root 34408 Feb 7 02:38 more - -rwsr-xr-x 1 root root 34400 Feb 7 02:38 mount - -rwxr-xr-x 1 root root 9824 Feb 7 02:38 mountpoint - -rwxr-xr-x 1 root root 88524 Sep 22 2020 mv - lrwxrwxrwx 1 root root 8 Nov 6 2019 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Apr 18 03:38 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 26652 Sep 22 2020 pwd - lrwxrwxrwx 1 root root 4 Jun 21 14:26 rbash -> bash - -rwxr-xr-x 1 root root 30740 Sep 22 2020 readlink - -rwxr-xr-x 1 root root 43104 Sep 22 2020 rm - -rwxr-xr-x 1 root root 30732 Sep 22 2020 rmdir - -rwxr-xr-x 1 root root 14144 Sep 27 2020 run-parts - -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Jul 13 21:26 sh -> dash - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sleep - -rwxr-xr-x 1 root root 55360 Sep 22 2020 stty - -rwsr-xr-x 1 root root 46704 Feb 7 02:38 su - -rwxr-xr-x 1 root root 22532 Sep 22 2020 sync - -rwxr-xr-x 1 root root 340872 Feb 16 21:55 tar - -rwxr-xr-x 1 root root 9808 Sep 27 2020 tempfile - -rwxr-xr-x 1 root root 67696 Sep 22 2020 touch - -rwxr-xr-x 1 root root 22496 Sep 22 2020 true - -rwxr-xr-x 1 root root 9636 Feb 26 04:12 ulockmgr_server - -rwsr-xr-x 1 root root 22108 Feb 7 02:38 umount - -rwxr-xr-x 1 root root 22520 Sep 22 2020 uname - -rwxr-xr-x 2 root root 2346 Mar 2 11:30 uncompress - -rwxr-xr-x 1 root root 96764 Sep 22 2020 vdir - -rwxr-xr-x 1 root root 38512 Feb 7 02:38 wdctl - lrwxrwxrwx 1 root root 8 Nov 6 2019 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1984 Mar 2 11:30 zcat - -rwxr-xr-x 1 root root 1678 Mar 2 11:30 zcmp - -rwxr-xr-x 1 root root 5880 Mar 2 11:30 zdiff - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zegrep - -rwxr-xr-x 1 root root 29 Mar 2 11:30 zfgrep - -rwxr-xr-x 1 root root 2081 Mar 2 11:30 zforce - -rwxr-xr-x 1 root root 7585 Mar 2 11:30 zgrep - -rwxr-xr-x 1 root root 2206 Mar 2 11:30 zless - -rwxr-xr-x 1 root root 1842 Mar 2 11:30 zmore - -rwxr-xr-x 1 root root 4553 Mar 2 11:30 znew -I: user script /srv/workspace/pbuilder/22929/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 816764 Jun 22 16:26 bash + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2 + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep + -rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2 + -rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore + -rwxr-xr-x 1 root root 26668 Sep 23 2020 cat + -rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp + -rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod + -rwxr-xr-x 1 root root 43112 Sep 23 2020 chown + -rwxr-xr-x 1 root root 92616 Sep 23 2020 cp + -rwxr-xr-x 1 root root 75524 Dec 11 2020 dash + -rwxr-xr-x 1 root root 75880 Sep 23 2020 date + -rwxr-xr-x 1 root root 55436 Sep 23 2020 dd + -rwxr-xr-x 1 root root 59912 Sep 23 2020 df + -rwxr-xr-x 1 root root 96764 Sep 23 2020 dir + -rwxr-xr-x 1 root root 55012 Feb 8 04:38 dmesg + lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname + -rwxr-xr-x 1 root root 22508 Sep 23 2020 echo + -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep + -rwxr-xr-x 1 root root 22496 Sep 23 2020 false + -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep + -rwxr-xr-x 1 root root 47492 Feb 8 04:38 findmnt + -rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount + -rwxr-xr-x 1 root root 124508 Nov 10 2020 grep + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip + -rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe + -rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip + -rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname + -rwxr-xr-x 1 root root 43180 Sep 23 2020 ln + -rwxr-xr-x 1 root root 35068 Feb 8 2020 login + -rwxr-xr-x 1 root root 96764 Sep 23 2020 ls + -rwxr-xr-x 1 root root 99940 Feb 8 04:38 lsblk + -rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir + -rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod + -rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp + -rwxr-xr-x 1 root root 34408 Feb 8 04:38 more + -rwsr-xr-x 1 root root 34400 Feb 8 04:38 mount + -rwxr-xr-x 1 root root 9824 Feb 8 04:38 mountpoint + -rwxr-xr-x 1 root root 88524 Sep 23 2020 mv + lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd + lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash + -rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink + -rwxr-xr-x 1 root root 43104 Sep 23 2020 rm + -rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir + -rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts + -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Jul 16 13:56 sh -> bash + lrwxrwxrwx 1 root root 4 Jul 13 23:26 sh.distrib -> dash + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep + -rwxr-xr-x 1 root root 55360 Sep 23 2020 stty + -rwsr-xr-x 1 root root 46704 Feb 8 04:38 su + -rwxr-xr-x 1 root root 22532 Sep 23 2020 sync + -rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar + -rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile + -rwxr-xr-x 1 root root 67696 Sep 23 2020 touch + -rwxr-xr-x 1 root root 22496 Sep 23 2020 true + -rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server + -rwsr-xr-x 1 root root 22108 Feb 8 04:38 umount + -rwxr-xr-x 1 root root 22520 Sep 23 2020 uname + -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress + -rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir + -rwxr-xr-x 1 root root 38512 Feb 8 04:38 wdctl + lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat + -rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp + -rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep + -rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep + -rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce + -rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep + -rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless + -rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore + -rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew +I: user script /srv/workspace/pbuilder/2929/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -253,7 +287,7 @@ Get: 50 http://deb.debian.org/debian bullseye/main armhf ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get: 51 http://deb.debian.org/debian bullseye/main armhf ncbi-blast+ armhf 2.11.0+ds-1 [9741 kB] Get: 52 http://deb.debian.org/debian bullseye/main armhf ncbi-blast+-legacy all 2.11.0+ds-1 [13.1 kB] -Fetched 36.7 MB in 4s (10.4 MB/s) +Fetched 36.7 MB in 20s (1828 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package bsdextrautils. (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 ... 19398 files and directories currently installed.) @@ -478,8 +512,45 @@ Writing extended state information... Building tag database... -> Finished parsing the build-deps +Reading package lists... +Building dependency tree... +Reading state information... +The following additional packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl +The following NEW packages will be installed: + libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge +0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. +Need to get 59.5 kB of archives. +After this operation, 157 kB of additional disk space will be used. +Get:1 http://deb.debian.org/debian bullseye/main armhf libnumber-compare-perl all 0.03-1.1 [6956 B] +Get:2 http://deb.debian.org/debian bullseye/main armhf libtext-glob-perl all 0.11-1 [8888 B] +Get:3 http://deb.debian.org/debian bullseye/main armhf libfile-find-rule-perl all 0.34-1 [30.6 kB] +Get:4 http://deb.debian.org/debian bullseye/main armhf usrmerge all 25 [13.0 kB] +debconf: delaying package configuration, since apt-utils is not installed +Fetched 59.5 kB in 1s (68.8 kB/s) +Selecting previously unselected package libnumber-compare-perl. +(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 ... 22291 files and directories currently installed.) +Preparing to unpack .../libnumber-compare-perl_0.03-1.1_all.deb ... +Unpacking libnumber-compare-perl (0.03-1.1) ... +Selecting previously unselected package libtext-glob-perl. +Preparing to unpack .../libtext-glob-perl_0.11-1_all.deb ... +Unpacking libtext-glob-perl (0.11-1) ... +Selecting previously unselected package libfile-find-rule-perl. +Preparing to unpack .../libfile-find-rule-perl_0.34-1_all.deb ... +Unpacking libfile-find-rule-perl (0.34-1) ... +Selecting previously unselected package usrmerge. +Preparing to unpack .../archives/usrmerge_25_all.deb ... +Unpacking usrmerge (25) ... +Setting up libtext-glob-perl (0.11-1) ... +Setting up libnumber-compare-perl (0.03-1.1) ... +Setting up libfile-find-rule-perl (0.34-1) ... +Setting up usrmerge (25) ... +The system has been successfully converted. +Processing triggers for man-db (2.9.4-2) ... +Not building database; man-db/auto-update is not 'true'. I: Building the package -I: Running cd /build/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+dfsg1-4_source.changes +hostname: Name or service not known +I: Running cd /build/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+dfsg1-4_source.changes dpkg-buildpackage: info: source package microbiomeutil dpkg-buildpackage: info: source version 20101212+dfsg1-4 dpkg-buildpackage: info: source distribution unstable @@ -491,7 +562,7 @@ debian/rules override_dh_auto_clean make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_clean - make -j5 clean + make -j4 clean make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ @@ -544,7 +615,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_build - make -j5 "INSTALL=install --strip-program=true" + make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ @@ -579,13 +650,13 @@ formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2>/dev/null -Building a new DB, current time: 07/15/2021 11:43:59 +Building a new DB, current time: 07/16/2021 13:57:04 New DB name: /build/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 1.78716 seconds. +Adding sequences from FASTA; added 5181 sequences in 0.811023 seconds. cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta @@ -594,7 +665,7 @@ debian/rules override_dh_auto_test make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_test - make -j5 test + make -j4 test make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1' cd NAST-iEr; make test cd WigeoN; make test @@ -608,43 +679,37 @@ cd ./sample_data; make test cd ./sample_data; make test cd ./sample_data; make test +make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' # -make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' -make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' # +make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' # +#************* TESTING WigeoN ********************" #*************** TESTING NAST-iEr *********************** #********** TESTING Chimera Slayer *************" -#************* TESTING WigeoN ********************" # # # -./testForUtils.pl ./runMe.sh ./runMe.sh +./testForUtils.pl ./runMe.sh query to NAST format -../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST - - -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 +../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST\n\n Can't locate Fasta_reader.pm in @INC (you may need to install the Fasta_reader module) (@INC contains: /usr/lib/WigeoN/PerlLib /etc/perl /usr/local/lib/arm-linux-gnueabihf/perl/5.32.1 /usr/local/share/perl/5.32.1 /usr/lib/arm-linux-gnueabihf/perl5/5.32 /usr/share/perl5 /usr/lib/arm-linux-gnueabihf/perl-base /usr/lib/arm-linux-gnueabihf/perl/5.32 /usr/share/perl/5.32 /usr/local/lib/site_perl) at ../run_WigeoN.pl line 13. BEGIN failed--compilation aborted at ../run_WigeoN.pl line 13. +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 make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/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/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 Num template seqs to align to: 2 Alignment parameters: MATCH: 5 @@ -654,35 +719,35 @@ Highest score: 11681 make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' - T(1)=6 s -ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 6 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 - T(1)=6 s -ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 6 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 - T(1)=6 s -ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 6 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 - T(1)=4 s -ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 4 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 + T(1)=3 s +ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 3 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 + T(1)=3 s +ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 3 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 + T(1)=2 s +ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 2 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 T(1)=2 s -ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 2 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 - T(1)=7 s -ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 7 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 - T(1)=5 s -ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 5 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 - T(1)=4 s -ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 4 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 - T(1)=4 s -ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 4 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.26039.query --db_NAST /tmp/tmp.26039.db -R 1.007 - T(1)=6 s -ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 6 seconds +ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 2 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 + T(1)=1 s +ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 1 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 + T(1)=3 s +ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 3 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 + T(1)=2 s +ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 2 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 + T(1)=2 s +ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 2 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 + T(1)=1 s +ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.6675.query --db_NAST /tmp/tmp.6675.db -R 1.007 + T(1)=3 s +ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 3 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 @@ -757,56 +822,56 @@ 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/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (7000004128191580, S000428666) or (0, 1) took 21 seconds -ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 58 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000378387, S000016146) or (0, 1) took 22 seconds -ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 48 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (7000004131500344, S000127669) or (0, 1) took 21 seconds -ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 40 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000004801, S000437365) or (0, 1) took 20 seconds -ChimeraSlayer(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 45 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000437007, S000437299) or (0, 1) took 21 seconds -ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 37 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000414109, S000253432) or (0, 1) took 18 seconds -ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 42 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (7000004131502379, 7000004128198963) or (0, 1) took 24 seconds -ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 65 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000503167, S000004272) or (0, 1) took 19 seconds -ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 30 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000436014, 7000004128189973) or (0, 1) took 18 seconds -ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 29 seconds -/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.2663.query --db_NAST /tmp/tmp.2663.db -P 90 -R 1.007 --minBS 90 --printAlignments - examined parents (S000009720, S000437236) or (0, 1) took 19 seconds -ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 43 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (7000004128191580, S000428666) or (0, 1) took 8 seconds +ChimeraSlayer(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 23 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.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 19 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (7000004131500344, S000127669) or (0, 1) took 8 seconds +ChimeraSlayer(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 17 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.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 20 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.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 16 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.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 17 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (7000004131502379, 7000004128198963) or (0, 1) took 10 seconds +ChimeraSlayer(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 29 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000503167, S000004272) or (0, 1) took 8 seconds +ChimeraSlayer(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 14 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.db -P 90 -R 1.007 --minBS 90 --printAlignments + examined parents (S000436014, 7000004128189973) or (0, 1) took 7 seconds +ChimeraSlayer(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 12 seconds +/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.7109.query --db_NAST /tmp/tmp.7109.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 22 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)=0 s -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)=1 s -ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 1 seconds +ChimeraParentSelector(chmraD24_7000004128191580_1-4580:4581-7682_S000428666) took 1 seconds T(1)=0 s -ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds - T(1)=1 s -ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 1 seconds +ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 0 seconds + T(1)=0 s +ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 seconds T(1)=1 s -ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 1 seconds +ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds T(1)=0 s -ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) took 0 seconds +ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds T(1)=0 s -ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds +ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 0 seconds T(1)=1 s -ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 seconds +ChimeraParentSelector(chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963) 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 ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 1 seconds make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' @@ -875,18 +940,18 @@ dh_shlibdeps -a dh_installdeb dh_gencontrol -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 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 chimeraslayer: 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 dh_md5sums dh_builddeb -dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-4_all.deb'. dpkg-deb: building package 'nast-ier' in '../nast-ier_20101212+dfsg1-4_armhf.deb'. dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-4_all.deb'. -dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-4_all.deb'. +dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-4_all.deb'. dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-4_armhf.deb'. +dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-4_all.deb'. dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-4_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../microbiomeutil_20101212+dfsg1-4_armhf.changes @@ -895,12 +960,14 @@ 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/2929/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2929/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/22929 and its subdirectories -I: Current time: Thu Jul 15 11:55:25 -12 2021 -I: pbuilder-time-stamp: 1626393325 +I: removing directory /srv/workspace/pbuilder/2929 and its subdirectories +I: Current time: Fri Jul 16 14:02:02 +14 2021 +I: pbuilder-time-stamp: 1626393722