I: pbuilder: network access will be disabled during build I: Current time: Mon Jul 20 20:39:07 -12 2020 I: pbuilder-time-stamp: 1595320747 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [microbiomeutil_20101212+dfsg1-2.dsc] I: copying [./microbiomeutil_20101212+dfsg1.orig.tar.xz] I: copying [./microbiomeutil_20101212+dfsg1-2.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/var/lib/jenkins/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Wed Jul 4 22:10:34 2018 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./microbiomeutil_20101212+dfsg1-2.dsc dpkg-source: info: extracting microbiomeutil in microbiomeutil-20101212+dfsg1 dpkg-source: info: unpacking microbiomeutil_20101212+dfsg1.orig.tar.xz dpkg-source: info: unpacking microbiomeutil_20101212+dfsg1-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_perl_interpreter.patch dpkg-source: info: applying find_relocated_resources.patch dpkg-source: info: applying find_relocated_libraries.patch dpkg-source: info: applying hardening.patch dpkg-source: info: applying enable_tests_in_local_dir.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/17838/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' 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='17838' PS1='# ' PS2='> ' 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.enqX6mmIuZ/pbuilderrc_SYzU --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.enqX6mmIuZ/b1 --logfile b1/build.log microbiomeutil_20101212+dfsg1-2.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink-sled14-arm64 4.4.0-185-generic #215-Ubuntu SMP Mon Jun 8 21:55:24 UTC 2020 aarch64 GNU/Linux I: ls -l /bin total 4928 -rwxr-xr-x 1 root root 1216928 Apr 17 2019 bash -rwxr-xr-x 3 root root 34808 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 34808 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 14264 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 35576 Feb 28 2019 cat -rwxr-xr-x 1 root root 60256 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 56096 Feb 28 2019 chmod -rwxr-xr-x 1 root root 64368 Feb 28 2019 chown -rwxr-xr-x 1 root root 134632 Feb 28 2019 cp -rwxr-xr-x 1 root root 129536 Jan 17 2019 dash -rwxr-xr-x 1 root root 97136 Feb 28 2019 date -rwxr-xr-x 1 root root 76736 Feb 28 2019 dd -rwxr-xr-x 1 root root 93752 Feb 28 2019 df -rwxr-xr-x 1 root root 138848 Feb 28 2019 dir -rwxr-xr-x 1 root root 75984 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 31368 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 27256 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 68792 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 34824 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 174304 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 89656 Jan 5 2019 gzip -rwxr-xr-x 1 root root 18440 Sep 26 2018 hostname -rwxr-xr-x 1 root root 64472 Feb 28 2019 ln -rwxr-xr-x 1 root root 52544 Jul 26 2018 login -rwxr-xr-x 1 root root 138848 Feb 28 2019 ls -rwxr-xr-x 1 root root 108552 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 76840 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 64480 Feb 28 2019 mknod -rwxr-xr-x 1 root root 39736 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 38840 Jan 9 2019 more -rwsr-xr-x 1 root root 47112 Jan 9 2019 mount -rwxr-xr-x 1 root root 14344 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 138736 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 35560 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 43712 Feb 28 2019 readlink -rwxr-xr-x 1 root root 68440 Feb 28 2019 rm -rwxr-xr-x 1 root root 39624 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 19144 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 114016 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Jul 19 20:27 sh -> dash -rwxr-xr-x 1 root root 31384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 72480 Feb 28 2019 stty -rwsr-xr-x 1 root root 59424 Jan 9 2019 su -rwxr-xr-x 1 root root 31416 Feb 28 2019 sync -rwxr-xr-x 1 root root 449416 Apr 23 2019 tar -rwxr-xr-x 1 root root 10560 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 88968 Feb 28 2019 touch -rwxr-xr-x 1 root root 27256 Feb 28 2019 true -rwxr-xr-x 1 root root 14264 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 30728 Jan 9 2019 umount -rwxr-xr-x 1 root root 31384 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 138848 Feb 28 2019 vdir -rwxr-xr-x 1 root root 34824 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/17838/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), cdbfasta, blast2 dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19168 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on cdbfasta; however: Package cdbfasta is not installed. pbuilder-satisfydepends-dummy depends on blast2; however: Package blast2 is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blast2{a} bsdmainutils{a} cdbfasta{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libbsd0{a} libcroco3{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libglib2.0-0{a} libicu63{a} liblmdb0{a} libmagic-mgc{a} libmagic1{a} libmbedcrypto3{a} libmbedtls12{a} libmbedx509-0{a} libncurses6{a} libpipeline1{a} libpython-stdlib{a} libpython2-stdlib{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} mime-support{a} ncbi-blast+{a} ncbi-blast+-legacy{a} ncbi-data{a} po-debconf{a} python{a} python-minimal{a} python2{a} python2-minimal{a} python2.7{a} python2.7-minimal{a} readline-common{a} sensible-utils{a} The following packages are RECOMMENDED but will NOT be installed: curl libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl lynx shared-mime-info wget xdg-user-dirs 0 packages upgraded, 57 newly installed, 0 to remove and 0 not upgraded. Need to get 38.0 MB of archives. After unpacking 162 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main arm64 libbsd0 arm64 0.9.1-2 [97.4 kB] Get: 2 http://deb.debian.org/debian buster/main arm64 bsdmainutils arm64 11.1.2+b1 [185 kB] Get: 3 http://deb.debian.org/debian buster/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get: 4 http://deb.debian.org/debian buster/main arm64 groff-base arm64 1.22.4-3 [869 kB] Get: 5 http://deb.debian.org/debian buster/main arm64 libpipeline1 arm64 1.5.1-2 [29.8 kB] Get: 6 http://deb.debian.org/debian buster/main arm64 man-db arm64 2.8.5-2 [1258 kB] Get: 7 http://deb.debian.org/debian buster/main arm64 libpython2.7-minimal arm64 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main arm64 python2.7-minimal arm64 2.7.16-2+deb10u1 [1292 kB] Get: 9 http://deb.debian.org/debian buster/main arm64 python2-minimal arm64 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main arm64 python-minimal arm64 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main arm64 libssl1.1 arm64 1.1.1d-0+deb10u3 [1382 kB] Get: 12 http://deb.debian.org/debian buster/main arm64 mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main arm64 libexpat1 arm64 2.2.6-2+deb10u1 [85.4 kB] Get: 14 http://deb.debian.org/debian buster/main arm64 readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main arm64 libreadline7 arm64 7.0-5 [134 kB] Get: 16 http://deb.debian.org/debian buster/main arm64 libpython2.7-stdlib arm64 2.7.16-2+deb10u1 [1890 kB] Get: 17 http://deb.debian.org/debian buster/main arm64 python2.7 arm64 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main arm64 libpython2-stdlib arm64 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main arm64 libpython-stdlib arm64 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main arm64 python2 arm64 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main arm64 python arm64 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main arm64 sensible-utils all 0.0.12 [15.8 kB] Get: 23 http://deb.debian.org/debian buster/main arm64 libmagic-mgc arm64 1:5.35-4+deb10u1 [242 kB] Get: 24 http://deb.debian.org/debian buster/main arm64 libmagic1 arm64 1:5.35-4+deb10u1 [115 kB] Get: 25 http://deb.debian.org/debian buster/main arm64 file arm64 1:5.35-4+deb10u1 [66.4 kB] Get: 26 http://deb.debian.org/debian buster/main arm64 gettext-base arm64 0.19.8.1-9 [120 kB] Get: 27 http://deb.debian.org/debian buster/main arm64 libsigsegv2 arm64 2.12-2 [32.3 kB] Get: 28 http://deb.debian.org/debian buster/main arm64 m4 arm64 1.4.18-2 [198 kB] Get: 29 http://deb.debian.org/debian buster/main arm64 autoconf all 2.69-11 [341 kB] Get: 30 http://deb.debian.org/debian buster/main arm64 autotools-dev all 20180224.1 [77.0 kB] Get: 31 http://deb.debian.org/debian buster/main arm64 automake all 1:1.16.1-4 [771 kB] Get: 32 http://deb.debian.org/debian buster/main arm64 autopoint all 0.19.8.1-9 [434 kB] Get: 33 http://deb.debian.org/debian buster/main arm64 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get: 34 http://deb.debian.org/debian buster/main arm64 liblmdb0 arm64 0.9.22-1 [40.3 kB] Get: 35 http://deb.debian.org/debian buster/main arm64 libmbedcrypto3 arm64 2.16.0-1 [202 kB] Get: 36 http://deb.debian.org/debian buster/main arm64 libmbedx509-0 arm64 2.16.0-1 [90.5 kB] Get: 37 http://deb.debian.org/debian buster/main arm64 libmbedtls12 arm64 2.16.0-1 [123 kB] Get: 38 http://deb.debian.org/debian buster/main arm64 ncbi-blast+ arm64 2.8.1-1+deb10u1 [9554 kB] Get: 39 http://deb.debian.org/debian buster/main arm64 ncbi-blast+-legacy all 2.8.1-1+deb10u1 [10.6 kB] Get: 40 http://deb.debian.org/debian buster/main arm64 blast2 all 1:2.8.1-1+deb10u1 [10.1 kB] Get: 41 http://deb.debian.org/debian buster/main arm64 cdbfasta arm64 0.99-20100722-5 [53.9 kB] Get: 42 http://deb.debian.org/debian buster/main arm64 libtool all 2.4.6-9 [547 kB] Get: 43 http://deb.debian.org/debian buster/main arm64 dh-autoreconf all 19 [16.9 kB] Get: 44 http://deb.debian.org/debian buster/main arm64 libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 45 http://deb.debian.org/debian buster/main arm64 libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 46 http://deb.debian.org/debian buster/main arm64 dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 47 http://deb.debian.org/debian buster/main arm64 libelf1 arm64 0.176-1.1 [160 kB] Get: 48 http://deb.debian.org/debian buster/main arm64 dwz arm64 0.12-3 [71.7 kB] Get: 49 http://deb.debian.org/debian buster/main arm64 libglib2.0-0 arm64 2.58.3-2+deb10u2 [1185 kB] Get: 50 http://deb.debian.org/debian buster/main arm64 libicu63 arm64 63.1-6+deb10u1 [8151 kB] Get: 51 http://deb.debian.org/debian buster/main arm64 libxml2 arm64 2.9.4+dfsg1-7+b3 [623 kB] Get: 52 http://deb.debian.org/debian buster/main arm64 libcroco3 arm64 0.6.12-3 [140 kB] Get: 53 http://deb.debian.org/debian buster/main arm64 libncurses6 arm64 6.1+20181013-2+deb10u2 [92.6 kB] Get: 54 http://deb.debian.org/debian buster/main arm64 gettext arm64 0.19.8.1-9 [1261 kB] Get: 55 http://deb.debian.org/debian buster/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 56 http://deb.debian.org/debian buster/main arm64 po-debconf all 1.0.21 [248 kB] Get: 57 http://deb.debian.org/debian buster/main arm64 debhelper all 12.1.1 [1016 kB] Fetched 38.0 MB in 4s (10.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:arm64. (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 ... 19168 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_arm64.deb ... Unpacking libbsd0:arm64 (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_arm64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../02-libuchardet0_0.0.6-3_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-3_arm64.deb ... Unpacking groff-base (1.22.4-3) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../04-libpipeline1_1.5.1-2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.1-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.8.5-2_arm64.deb ... Unpacking man-db (2.8.5-2) ... Selecting previously unselected package libpython2.7-minimal:arm64. Preparing to unpack .../06-libpython2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../07-python2.7-minimal_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7-minimal (2.7.16-2+deb10u1) ... Selecting previously unselected package python2-minimal. Preparing to unpack .../08-python2-minimal_2.7.16-1_arm64.deb ... Unpacking python2-minimal (2.7.16-1) ... Selecting previously unselected package python-minimal. Preparing to unpack .../09-python-minimal_2.7.16-1_arm64.deb ... Unpacking python-minimal (2.7.16-1) ... Selecting previously unselected package libssl1.1:arm64. Preparing to unpack .../10-libssl1.1_1.1.1d-0+deb10u3_arm64.deb ... Unpacking libssl1.1:arm64 (1.1.1d-0+deb10u3) ... Selecting previously unselected package mime-support. Preparing to unpack .../11-mime-support_3.62_all.deb ... Unpacking mime-support (3.62) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../12-libexpat1_2.2.6-2+deb10u1_arm64.deb ... Unpacking libexpat1:arm64 (2.2.6-2+deb10u1) ... Selecting previously unselected package readline-common. Preparing to unpack .../13-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libreadline7:arm64. Preparing to unpack .../14-libreadline7_7.0-5_arm64.deb ... Unpacking libreadline7:arm64 (7.0-5) ... Selecting previously unselected package libpython2.7-stdlib:arm64. Preparing to unpack .../15-libpython2.7-stdlib_2.7.16-2+deb10u1_arm64.deb ... Unpacking libpython2.7-stdlib:arm64 (2.7.16-2+deb10u1) ... Selecting previously unselected package python2.7. Preparing to unpack .../16-python2.7_2.7.16-2+deb10u1_arm64.deb ... Unpacking python2.7 (2.7.16-2+deb10u1) ... Selecting previously unselected package libpython2-stdlib:arm64. Preparing to unpack .../17-libpython2-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython2-stdlib:arm64 (2.7.16-1) ... Selecting previously unselected package libpython-stdlib:arm64. Preparing to unpack .../18-libpython-stdlib_2.7.16-1_arm64.deb ... Unpacking libpython-stdlib:arm64 (2.7.16-1) ... Setting up libpython2.7-minimal:arm64 (2.7.16-2+deb10u1) ... Setting up python2.7-minimal (2.7.16-2+deb10u1) ... Setting up python2-minimal (2.7.16-1) ... Selecting previously unselected package python2. (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 ... 20631 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_arm64.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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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 dpkg-buildpackage: info: source package microbiomeutil dpkg-buildpackage: info: source version 20101212+dfsg1-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_clean make -j8 clean make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ do echo '<<<' $i '>>>'; cd $X/$i; make clean; done <<< NAST-iEr >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make clean make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f tmp.* make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' rm -f NAST-iEr make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make clean make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' rm -f chims.NAST.* rm -f sample_DB.NAST.cidx rm -f sample_DB.fasta.* rm -f tmp.* rm -f formatdb.log make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make clean make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' rm -f tmp.* rm -f chims.NAST.* make[4]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/RESOURCES' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. rm -f *fasta.* make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx rm -f formatdb.log make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_build make -j8 "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1' X=`pwd`; \ for i in NAST-iEr ChimeraSlayer WigeoN RESOURCES; \ do echo '<<<' $i '>>>'; cd $X/$i; make all; done <<< NAST-iEr >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/build/microbiomeutil-20101212+dfsg1=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now NAST-iEr.c -o NAST-iEr NAST-iEr.c: In function 'main': NAST-iEr.c:106:8: warning: implicit declaration of function 'isprint' [-Wimplicit-function-declaration] if (isprint (optopt)) { ^~~~~~~ make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' <<< ChimeraSlayer >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' <<< WigeoN >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' <<< RESOURCES >>> make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/RESOURCES' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/RESOURCES' make[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' #Pre-make indexes for ChimeraSlayer, otherwise it tries to write them #to the non-writeable dir on first run and blows up formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2>/dev/null Building a new DB, current time: 07/20/2020 20:39:58 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 1.06647 seconds. cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta 5181 entries from file RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta were indexed in file RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta.cidx make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' debian/rules override_dh_auto_test make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_auto_test make -j8 test make[2]: Entering directory '/build/microbiomeutil-20101212+dfsg1' cd NAST-iEr; make test cd WigeoN; make test make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make test cd ChimeraSlayer; make test make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/NAST-iEr/sample_data' # make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make test make[3]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. cd ./sample_data; make test #*************** TESTING NAST-iEr *********************** make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/sample_data' # # make[4]: Entering directory '/build/microbiomeutil-20101212+dfsg1/WigeoN/sample_data' # ./testForUtils.pl #********** TESTING Chimera Slayer *************" #************* TESTING WigeoN ********************" # # ./runMe.sh ./runMe.sh ./runMe.sh query to NAST format ../NAST-iEr template_seqs.NAST query_seq.fasta > tmp.query.NAST 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/aarch64-linux-gnu/perl/5.28.1 /usr/local/share/perl/5.28.1 /usr/lib/aarch64-linux-gnu/perl5/5.28 /usr/share/perl5 /usr/lib/aarch64-linux-gnu/perl/5.28 /usr/share/perl/5.28 /usr/local/lib/site_perl /usr/lib/aarch64-linux-gnu/perl-base) 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 converting NAST mfasta to multi-alignment output highlighting differences ../show_malign_no_gap.pl --IGNOREGAPS tmp.both.NAST > tmp.both.NAST.malign Run via the megablast wrapper Num template seqs to align to: 2 Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19177.query --db_NAST /tmp/tmp.19177.db -R 1.007 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)=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.19177.query --db_NAST /tmp/tmp.19177.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 2 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19177.query --db_NAST /tmp/tmp.19177.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.19177.query --db_NAST /tmp/tmp.19177.db -R 1.007 T(1)=1 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 1 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19177.query --db_NAST /tmp/tmp.19177.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.19177.query --db_NAST /tmp/tmp.19177.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 2 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19177.query --db_NAST /tmp/tmp.19177.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.19177.query --db_NAST /tmp/tmp.19177.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.19177.query --db_NAST /tmp/tmp.19177.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 2 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraParentSelector/chimeraParentSelector.pl --query_NAST /tmp/tmp.19177.query --db_NAST /tmp/tmp.19177.db -R 1.007 T(1)=2 s ChimeraParentSelector(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 2 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 Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 10945 processing: ChimeraParentSelector chmraD19_S000378387_1-5075:5076-7682_S000016146 YES 100.00[(S000378387, NAST:443-5077, ECO:94-1125, RawLen:1041, G:96.08, L:100.00, 1.041);(S000016146, NAST:5079-6498, ECO:1126-1424, RawLen:301, G:85.08, L:100.00, 1.175)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 12151 processing: ChimeraParentSelector chmraD12_7000004131500344_1-4694:4695-7682_S000127669 YES 100.00[(7000004131500344, NAST:426-4710, ECO:86-999, RawLen:914, G:96.38, L:100.00, 1.038);(S000127669, NAST:4711-6711, ECO:999-1451, RawLen:453, G:92.52, L:100.00, 1.081)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 12852 processing: ChimeraParentSelector chmraD13_S000004801_1-4690:4691-7682_S000437365 YES 100.00[(S000004801, NAST:455-4707, ECO:101-997, RawLen:913, G:96.34, L:100.00, 1.038);(S000437365, NAST:4708-6424, ECO:997-1382, RawLen:391, G:90.85, L:100.00, 1.101)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 12579 processing: ChimeraParentSelector chmraD9_S000437007_1-4525:4526-7682_S000437299 YES 100.00[(S000437007, NAST:164-4657, ECO:36-982, RawLen:903, G:96.21, L:100.00, 1.039);(S000437299, NAST:4658-6422, ECO:983-1380, RawLen:401, G:94.45, L:100.00, 1.059)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 13167 processing: ChimeraParentSelector chmraD17_S000414109_1-4650:4651-7682_S000253432 YES 100.00[(S000414109, NAST:153-4671, ECO:31-990, RawLen:907, G:94.16, L:100.00, 1.062);(S000253432, NAST:4673-6716, ECO:991-1453, RawLen:462, G:88.62, L:100.00, 1.128)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 11650 processing: ChimeraParentSelector chmraD22_7000004131502379_1-4625:4626-7682_7000004128198963 YES 100.00[(7000004131502379, NAST:489-4623, ECO:115-959, RawLen:851, G:92.66, L:100.00, 1.079);(7000004128198963, NAST:4625-6422, ECO:961-1380, RawLen:422, G:84.94, L:100.00, 1.177)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 11807 processing: ChimeraParentSelector chmraD8_S000004272_1-3794:3795-7682_S000503167 YES 100.00[(S000004272, NAST:162-3829, ECO:35-701, RawLen:668, G:95.64, L:100.00, 1.046);(S000503167, NAST:3831-6464, ECO:702-1405, RawLen:705, G:95.81, L:100.00, 1.044)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 13234 processing: ChimeraParentSelector chmraD11_S000436014_1-5755:5756-7682_7000004128189973 YES 100.00[(S000436014, NAST:428-5920, ECO:88-1237, RawLen:1122, G:97.80, L:100.00, 1.022);(7000004128189973, NAST:5921-6521, ECO:1238-1435, RawLen:200, G:91.75, L:100.00, 1.090)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 Highest score: 12609 processing: ChimeraParentSelector chmraD23_S000009720_1-5056:5057-7682_S000437236 YES 100.00[(S000009720, NAST:184-5057, ECO:47-1116, RawLen:1079, G:96.18, L:100.00, 1.040);(S000437236, NAST:5058-6474, ECO:1117-1411, RawLen:296, G:81.53, L:100.00, 1.227)] Alignment parameters: MATCH: 5 MISMATCH: -4 GAP: -4 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.21189.query --db_NAST /tmp/tmp.21189.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 22 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.21189.query --db_NAST /tmp/tmp.21189.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000378387, S000016146) or (0, 1) took 8 seconds ChimeraSlayer(chmraD19_S000378387_1-5075:5076-7682_S000016146) took 19 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.21189.query --db_NAST /tmp/tmp.21189.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 16 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.21189.query --db_NAST /tmp/tmp.21189.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 18 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.21189.query --db_NAST /tmp/tmp.21189.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000437007, S000437299) or (0, 1) took 8 seconds ChimeraSlayer(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 15 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.21189.query --db_NAST /tmp/tmp.21189.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000414109, S000253432) or (0, 1) took 7 seconds ChimeraSlayer(chmraD17_S000414109_1-4650:4651-7682_S000253432) took 16 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.21189.query --db_NAST /tmp/tmp.21189.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 26 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.21189.query --db_NAST /tmp/tmp.21189.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 13 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.21189.query --db_NAST /tmp/tmp.21189.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 11 seconds /build/microbiomeutil-20101212+dfsg1/ChimeraSlayer/ChimeraPhyloChecker/ChimeraPhyloChecker.pl --query_NAST /tmp/tmp.21189.query --db_NAST /tmp/tmp.21189.db -P 90 -R 1.007 --minBS 90 --printAlignments examined parents (S000009720, S000437236) or (0, 1) took 7 seconds ChimeraSlayer(chmraD23_S000009720_1-5056:5057-7682_S000437236) took 18 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)=0 s ChimeraParentSelector(chmraD12_7000004131500344_1-4694:4695-7682_S000127669) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD13_S000004801_1-4690:4691-7682_S000437365) took 0 seconds T(1)=0 s ChimeraParentSelector(chmraD9_S000437007_1-4525:4526-7682_S000437299) took 0 seconds T(1)=1 s 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)=0 s ChimeraParentSelector(chmraD8_S000004272_1-3794:3795-7682_S000503167) took 0 seconds T(1)=1 s ChimeraParentSelector(chmraD11_S000436014_1-5755:5756-7682_7000004128189973) took 1 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' make[3]: Leaving directory '/build/microbiomeutil-20101212+dfsg1/ChimeraSlayer' make[2]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary dh_testroot dh_prep dh_auto_install debian/rules override_dh_install make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_install -XMakefile -Xsample_data -XLICENSE -XNAST-iEr.c make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' dh_installdocs dh_installchangelogs debian/rules override_dh_installexamples make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_installexamples for mod in ChimeraSlayer NAST-iEr WigeoN ; do \ mkdir -p /build/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod} ; \ cp -a ${mod}/sample_data/* /build/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod} ; \ sed -i -e "s?../${mod}?${mod}?" \ -e "s?^.*\(/util/show_malign_no_gap.pl\)?/usr/lib/NAST-iEr\1?" \ -e "s?^.*\(/run_NAST-iEr.pl\)?/usr/lib/NAST-iEr\1?" \ -e "s?^.*\(ChimeraSlayer.pl\)?/usr/lib/ChimeraSlayer/\1?" \ -e "s?^.*\(/run_WigeoN.pl\)?/usr/lib/WigeoN\1?" \ /build/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/${mod}/runMe.sh ; \ done sed -i '1i #!/bin/sh' /build/microbiomeutil-20101212+dfsg1/debian/microbiomeutil-data/usr/share/doc/microbiomeutil-data/examples/WigeoN/runMe.sh make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms make[1]: Entering directory '/build/microbiomeutil-20101212+dfsg1' dh_fixperms find debian -type f -name '*.pm' -print0 | xargs -0r chmod a-x find debian -type f -name 'genus_counter.pl' -print0 | xargs -0r chmod a+x make[1]: Leaving directory '/build/microbiomeutil-20101212+dfsg1' dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol 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 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 nast-ier: substitution variable ${perl:Depends} unused, but is defined dh_md5sums dh_builddeb dpkg-deb: building package 'chimeraslayer' in '../chimeraslayer_20101212+dfsg1-2_all.deb'. dpkg-deb: building package 'nast-ier' in '../nast-ier_20101212+dfsg1-2_arm64.deb'. dpkg-deb: building package 'microbiomeutil' in '../microbiomeutil_20101212+dfsg1-2_all.deb'. dpkg-deb: building package 'nast-ier-dbgsym' in '../nast-ier-dbgsym_20101212+dfsg1-2_arm64.deb'. dpkg-deb: building package 'microbiomeutil-data' in '../microbiomeutil-data_20101212+dfsg1-2_all.deb'. dpkg-deb: building package 'wigeon' in '../wigeon_20101212+dfsg1-2_all.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../microbiomeutil_20101212+dfsg1-2_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration 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/17838 and its subdirectories I: Current time: Mon Jul 20 20:44:53 -12 2020 I: pbuilder-time-stamp: 1595321093