I: pbuilder: network access will be disabled during build I: Current time: Wed Jul 7 11:06:53 +14 2021 I: pbuilder-time-stamp: 1625605613 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bullseye-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 [ariba_2.14.6+ds-1.dsc] I: copying [./ariba_2.14.6+ds.orig.tar.xz] I: copying [./ariba_2.14.6+ds-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/tmp/dpkg-verify-sig.SNzZtd6e/trustedkeys.kbx': General error gpgv: Signature made Mon Sep 14 07:03:27 2020 +14 gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ariba_2.14.6+ds-1.dsc dpkg-source: info: extracting ariba in ariba-2.14.6+ds dpkg-source: info: unpacking ariba_2.14.6+ds.orig.tar.xz dpkg-source: info: unpacking ariba_2.14.6+ds-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch dpkg-source: info: applying use_bwa_compatible_fermi-lite.patch dpkg-source: info: applying add-testdata.patch dpkg-source: info: applying disable-tests-with-internet-access.patch dpkg-source: info: applying support-pymummer-0.11.patch dpkg-source: info: applying run-debian-spades-wrapper.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/25398/tmp/hooks/D01_modify_environment starting debug: Running on codethink12-arm64. 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/25398/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/25398/tmp/hooks/D02_print_environment starting I: set 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]="aarch64-unknown-linux-gnu") 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=arm64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=8' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/var/lib/jenkins HOSTNAME=i-capture-the-hostname HOSTTYPE=aarch64 HOST_ARCH=arm64 IFS=' ' LANG=C LANGUAGE=nl_BE:nl LC_ALL=C MACHTYPE=aarch64-unknown-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=25398 PS4='+ ' 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.N7g0fmKknS/pbuilderrc_7nla --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.N7g0fmKknS/b2 --logfile b2/build.log --extrapackages usrmerge ariba_2.14.6+ds-1.dsc' SUDO_GID=117 SUDO_UID=110 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root USERNAME=root _='I: set' http_proxy=http://192.168.101.16:3128 I: uname -a Linux i-capture-the-hostname 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:18:37 UTC 2021 aarch64 GNU/Linux I: ls -l /bin total 5252 -rwxr-xr-x 1 root root 1282512 Jun 22 16:26 bash -rwxr-xr-x 3 root root 34808 Jul 21 2020 bunzip2 -rwxr-xr-x 3 root root 34808 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 34808 Jul 21 2020 bzip2 -rwxr-xr-x 1 root root 14264 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 39832 Sep 23 2020 cat -rwxr-xr-x 1 root root 64512 Sep 23 2020 chgrp -rwxr-xr-x 1 root root 60368 Sep 23 2020 chmod -rwxr-xr-x 1 root root 64528 Sep 23 2020 chown -rwxr-xr-x 1 root root 138896 Sep 23 2020 cp -rwxr-xr-x 1 root root 129544 Dec 11 2020 dash -rwxr-xr-x 1 root root 101384 Sep 23 2020 date -rwxr-xr-x 1 root root 80984 Sep 23 2020 dd -rwxr-xr-x 1 root root 89824 Sep 23 2020 df -rwxr-xr-x 1 root root 143088 Sep 23 2020 dir -rwxr-xr-x 1 root root 76152 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 35632 Sep 23 2020 echo -rwxr-xr-x 1 root root 28 Nov 10 2020 egrep -rwxr-xr-x 1 root root 31512 Sep 23 2020 false -rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep -rwxr-xr-x 1 root root 64856 Feb 8 04:38 findmnt -rwsr-xr-x 1 root root 34824 Feb 27 06:12 fusermount -rwxr-xr-x 1 root root 178400 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 93744 Mar 3 13:30 gzip -rwxr-xr-x 1 root root 18440 Nov 8 2019 hostname -rwxr-xr-x 1 root root 68720 Sep 23 2020 ln -rwxr-xr-x 1 root root 52720 Feb 8 2020 login -rwxr-xr-x 1 root root 143088 Sep 23 2020 ls -rwxr-xr-x 1 root root 161960 Feb 8 04:38 lsblk -rwxr-xr-x 1 root root 85200 Sep 23 2020 mkdir -rwxr-xr-x 1 root root 68744 Sep 23 2020 mknod -rwxr-xr-x 1 root root 43976 Sep 23 2020 mktemp -rwxr-xr-x 1 root root 51368 Feb 8 04:38 more -rwsr-xr-x 1 root root 51360 Feb 8 04:38 mount -rwxr-xr-x 1 root root 14496 Feb 8 04:38 mountpoint -rwxr-xr-x 1 root root 134808 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 35720 Sep 23 2020 pwd lrwxrwxrwx 1 root root 4 Jun 22 16:26 rbash -> bash -rwxr-xr-x 1 root root 43872 Sep 23 2020 readlink -rwxr-xr-x 1 root root 68592 Sep 23 2020 rm -rwxr-xr-x 1 root root 43880 Sep 23 2020 rmdir -rwxr-xr-x 1 root root 19208 Sep 28 2020 run-parts -rwxr-xr-x 1 root root 114016 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jul 7 11:07 sh -> bash lrwxrwxrwx 1 root root 4 Jul 5 23:25 sh.distrib -> dash -rwxr-xr-x 1 root root 35656 Sep 23 2020 sleep -rwxr-xr-x 1 root root 72640 Sep 23 2020 stty -rwsr-xr-x 1 root root 67776 Feb 8 04:38 su -rwxr-xr-x 1 root root 35672 Sep 23 2020 sync -rwxr-xr-x 1 root root 535768 Feb 17 23:55 tar -rwxr-xr-x 1 root root 10568 Sep 28 2020 tempfile -rwxr-xr-x 1 root root 89120 Sep 23 2020 touch -rwxr-xr-x 1 root root 31512 Sep 23 2020 true -rwxr-xr-x 1 root root 14264 Feb 27 06:12 ulockmgr_server -rwsr-xr-x 1 root root 30880 Feb 8 04:38 umount -rwxr-xr-x 1 root root 35640 Sep 23 2020 uname -rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress -rwxr-xr-x 1 root root 143088 Sep 23 2020 vdir -rwxr-xr-x 1 root root 59584 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/25398/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-compat (= 13), dh-python, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3-nose (>= 1.3), python3-bs4, python3-matplotlib, python3-tk, bowtie2 (>= 2.1.0), cd-hit, mash, libminimap-dev, libfml-dev (>= 0.1-4~), mummer, fastaq (>= 3.12.0), help2man, asciidoctor dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19646 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-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on python3-biopython; however: Package python3-biopython is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dendropy; however: Package python3-dendropy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pymummer (>= 0.10.2); however: Package python3-pymummer is not installed. pbuilder-satisfydepends-dummy depends on python3-pysam (>= 0.9.1); however: Package python3-pysam is not installed. pbuilder-satisfydepends-dummy depends on python3-nose (>= 1.3); however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-bs4; however: Package python3-bs4 is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-tk; however: Package python3-tk is not installed. pbuilder-satisfydepends-dummy depends on bowtie2 (>= 2.1.0); however: Package bowtie2 is not installed. pbuilder-satisfydepends-dummy depends on cd-hit; however: Package cd-hit is not installed. pbuilder-satisfydepends-dummy depends on mash; however: Package mash is not installed. pbuilder-satisfydepends-dummy depends on libminimap-dev; however: Package libminimap-dev is not installed. pbuilder-satisfydepends-dummy depends on libfml-dev (>= 0.1-4~); however: Package libfml-dev is not installed. pbuilder-satisfydepends-dummy depends on mummer; however: Package mummer is not installed. pbuilder-satisfydepends-dummy depends on fastaq (>= 3.12.0); however: Package fastaq is not installed. pbuilder-satisfydepends-dummy depends on help2man; however: Package help2man is not installed. pbuilder-satisfydepends-dummy depends on asciidoctor; however: Package asciidoctor 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: asciidoctor{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bowtie2{a} bsdextrautils{a} ca-certificates{a} cd-hit{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} fastaq{a} file{a} fontconfig-config{a} fonts-lyx{a} gawk{a} gettext{a} gettext-base{a} groff-base{a} help2man{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbrotli1{a} libbsd0{a} libcapnp-0.7.0{a} libcurl3-gnutls{a} libdebhelper-perl{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfml-dev{a} libfml0{a} libfontconfig1{a} libfreetype6{a} libgfortran5{a} libgsl25{a} libgslcblas0{a} libhts3{a} libicu67{a} libimagequant0{a} libjbig0{a} libjpeg62-turbo{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblcms2-2{a} libldap-2.4-2{a} liblocale-gettext-perl{a} libmagic-mgc{a} libmagic1{a} libmd0{a} libminimap-dev{a} libminimap0{a} libmpdec3{a} libmurmurhash2{a} libncurses6{a} libnghttp2-14{a} libpipeline1{a} libpng16-16{a} libpsl5{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.9{a} libpython3.9-dev{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libruby2.7{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libtiff5{a} libtk8.6{a} libtool{a} libuchardet0{a} libwebp6{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxft2{a} libxml2{a} libxrender1{a} libxss1{a} libyaml-0-2{a} m4{a} mailcap{a} man-db{a} mash{a} media-types{a} mime-support{a} mummer{a} openssl{a} po-debconf{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-biopython{a} python3-bs4{a} python3-cycler{a} python3-dateutil{a} python3-dendropy{a} python3-dev{a} python3-distutils{a} python3-kiwisolver{a} python3-lib2to3{a} python3-matplotlib{a} python3-minimal{a} python3-nose{a} python3-numpy{a} python3-pil{a} python3-pkg-resources{a} python3-pymummer{a} python3-pyparsing{a} python3-pysam{a} python3-reportlab{a} python3-reportlab-accel{a} python3-setuptools{a} python3-six{a} python3-soupsieve{a} python3-tk{a} python3.9{a} python3.9-dev{a} python3.9-minimal{a} rake{a} readline-common{a} ruby{a} ruby-asciidoctor{a} ruby-minitest{a} ruby-net-telnet{a} ruby-power-assert{a} ruby-rubygems{a} ruby-test-unit{a} ruby-xmlrpc{a} ruby2.7{a} rubygems-integration{a} samtools{a} sensible-utils{a} tk8.6-blt2.5{a} ttf-bitstream-vera{a} ucf{a} x11-common{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: curl fonts-lato javascript-common libarchive-cpio-perl libgpm2 libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx ncbi-blast+ publicsuffix python-biopython-doc python3-chardet python3-lxml python3-olefile python3-renderpm wget zip 0 packages upgraded, 163 newly installed, 0 to remove and 0 not upgraded. Need to get 70.8 MB of archives. After unpacking 263 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bullseye/main arm64 bsdextrautils arm64 2.36.1-7 [141 kB] Get: 2 http://deb.debian.org/debian bullseye/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 3 http://deb.debian.org/debian bullseye/main arm64 groff-base arm64 1.22.4-6 [883 kB] Get: 4 http://deb.debian.org/debian bullseye/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB] Get: 5 http://deb.debian.org/debian bullseye/main arm64 man-db arm64 2.9.4-2 [1336 kB] Get: 6 http://deb.debian.org/debian bullseye/main arm64 readline-common all 8.1-1 [73.7 kB] Get: 7 http://deb.debian.org/debian bullseye/main arm64 libreadline8 arm64 8.1-1 [160 kB] Get: 8 http://deb.debian.org/debian bullseye/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB] Get: 9 http://deb.debian.org/debian bullseye/main arm64 gawk arm64 1:5.1.0-1 [570 kB] Get: 10 http://deb.debian.org/debian bullseye/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB] Get: 11 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-minimal arm64 3.9.2-1 [797 kB] Get: 12 http://deb.debian.org/debian bullseye/main arm64 libexpat1 arm64 2.2.10-2 [83.1 kB] Get: 13 http://deb.debian.org/debian bullseye/main arm64 python3.9-minimal arm64 3.9.2-1 [1884 kB] Get: 14 http://deb.debian.org/debian bullseye/main arm64 python3-minimal arm64 3.9.2-3 [38.2 kB] Get: 15 http://deb.debian.org/debian bullseye/main arm64 media-types all 4.0.0 [30.3 kB] Get: 16 http://deb.debian.org/debian bullseye/main arm64 mailcap all 3.69 [31.7 kB] Get: 17 http://deb.debian.org/debian bullseye/main arm64 mime-support all 3.66 [10.9 kB] Get: 18 http://deb.debian.org/debian bullseye/main arm64 libmpdec3 arm64 2.5.1-1 [84.4 kB] Get: 19 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-stdlib arm64 3.9.2-1 [1658 kB] Get: 20 http://deb.debian.org/debian bullseye/main arm64 python3.9 arm64 3.9.2-1 [466 kB] Get: 21 http://deb.debian.org/debian bullseye/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB] Get: 22 http://deb.debian.org/debian bullseye/main arm64 python3 arm64 3.9.2-3 [37.9 kB] Get: 23 http://deb.debian.org/debian bullseye/main arm64 sensible-utils all 0.0.14 [14.8 kB] Get: 24 http://deb.debian.org/debian bullseye/main arm64 openssl arm64 1.1.1k-1 [829 kB] Get: 25 http://deb.debian.org/debian bullseye/main arm64 ca-certificates all 20210119 [158 kB] Get: 26 http://deb.debian.org/debian bullseye/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB] Get: 27 http://deb.debian.org/debian bullseye/main arm64 libmagic1 arm64 1:5.39-3 [121 kB] Get: 28 http://deb.debian.org/debian bullseye/main arm64 file arm64 1:5.39-3 [69.1 kB] Get: 29 http://deb.debian.org/debian bullseye/main arm64 gettext-base arm64 0.21-4 [173 kB] Get: 30 http://deb.debian.org/debian bullseye/main arm64 ucf all 3.0043 [74.0 kB] Get: 31 http://deb.debian.org/debian bullseye/main arm64 rubygems-integration all 1.18 [6704 B] Get: 32 http://deb.debian.org/debian bullseye/main arm64 rake all 13.0.3-1 [84.7 kB] Get: 33 http://deb.debian.org/debian bullseye/main arm64 ruby-minitest all 5.13.0-1 [57.3 kB] Get: 34 http://deb.debian.org/debian bullseye/main arm64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get: 35 http://deb.debian.org/debian bullseye/main arm64 ruby-power-assert all 1.1.7-2 [11.5 kB] Get: 36 http://deb.debian.org/debian bullseye/main arm64 ruby-test-unit all 3.3.9-1 [86.1 kB] Get: 37 http://deb.debian.org/debian bullseye/main arm64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get: 38 http://deb.debian.org/debian bullseye/main arm64 libmd0 arm64 1.0.3-3 [27.9 kB] Get: 39 http://deb.debian.org/debian bullseye/main arm64 libbsd0 arm64 0.11.3-1 [106 kB] Get: 40 http://deb.debian.org/debian bullseye/main arm64 libedit2 arm64 3.1-20191231-2+b1 [92.1 kB] Get: 41 http://deb.debian.org/debian bullseye/main arm64 libyaml-0-2 arm64 0.2.2-1 [45.1 kB] Get: 42 http://deb.debian.org/debian bullseye/main arm64 libruby2.7 arm64 2.7.3-2 [4026 kB] Get: 43 http://deb.debian.org/debian bullseye/main arm64 ruby2.7 arm64 2.7.3-2 [744 kB] Get: 44 http://deb.debian.org/debian bullseye/main arm64 ruby-rubygems all 3.2.5-2 [281 kB] Get: 45 http://deb.debian.org/debian bullseye/main arm64 ruby arm64 1:2.7+2 [11.7 kB] Get: 46 http://deb.debian.org/debian bullseye/main arm64 ruby-asciidoctor all 2.0.12-2 [206 kB] Get: 47 http://deb.debian.org/debian bullseye/main arm64 asciidoctor all 2.0.12-2 [83.9 kB] Get: 48 http://deb.debian.org/debian bullseye/main arm64 m4 arm64 1.4.18-5 [199 kB] Get: 49 http://deb.debian.org/debian bullseye/main arm64 autoconf all 2.69-14 [313 kB] Get: 50 http://deb.debian.org/debian bullseye/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB] Get: 51 http://deb.debian.org/debian bullseye/main arm64 automake all 1:1.16.3-2 [814 kB] Get: 52 http://deb.debian.org/debian bullseye/main arm64 autopoint all 0.21-4 [510 kB] Get: 53 http://deb.debian.org/debian bullseye/main arm64 libtcl8.6 arm64 8.6.11+dfsg-1 [964 kB] Get: 54 http://deb.debian.org/debian bullseye/main arm64 libbrotli1 arm64 1.0.9-2+b2 [267 kB] Get: 55 http://deb.debian.org/debian bullseye/main arm64 libpng16-16 arm64 1.6.37-3 [289 kB] Get: 56 http://deb.debian.org/debian bullseye/main arm64 libfreetype6 arm64 2.10.4+dfsg-1 [393 kB] Get: 57 http://deb.debian.org/debian bullseye/main arm64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get: 58 http://deb.debian.org/debian bullseye/main arm64 fontconfig-config all 2.13.1-4.2 [281 kB] Get: 59 http://deb.debian.org/debian bullseye/main arm64 libfontconfig1 arm64 2.13.1-4.2 [344 kB] Get: 60 http://deb.debian.org/debian bullseye/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 61 http://deb.debian.org/debian bullseye/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 62 http://deb.debian.org/debian bullseye/main arm64 libxcb1 arm64 1.14-3 [138 kB] Get: 63 http://deb.debian.org/debian bullseye/main arm64 libx11-data all 2:1.7.1-1 [310 kB] Get: 64 http://deb.debian.org/debian bullseye/main arm64 libx11-6 arm64 2:1.7.1-1 [747 kB] Get: 65 http://deb.debian.org/debian bullseye/main arm64 libxrender1 arm64 1:0.9.10-1 [30.4 kB] Get: 66 http://deb.debian.org/debian bullseye/main arm64 libxft2 arm64 2.3.2-2 [51.3 kB] Get: 67 http://deb.debian.org/debian bullseye/main arm64 libxext6 arm64 2:1.3.3-1.1 [51.6 kB] Get: 68 http://deb.debian.org/debian bullseye/main arm64 x11-common all 1:7.7+22 [252 kB] Get: 69 http://deb.debian.org/debian bullseye/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 70 http://deb.debian.org/debian bullseye/main arm64 libtk8.6 arm64 8.6.11-2 [738 kB] Get: 71 http://deb.debian.org/debian bullseye/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-4.1 [540 kB] Get: 72 http://deb.debian.org/debian bullseye/main arm64 blt arm64 2.5.3+dfsg-4.1 [14.9 kB] Get: 73 http://deb.debian.org/debian bullseye/main arm64 bowtie2 arm64 2.4.2-2+b3 [1264 kB] Get: 74 http://deb.debian.org/debian bullseye/main arm64 cd-hit arm64 4.8.1-3 [506 kB] Get: 75 http://deb.debian.org/debian bullseye/main arm64 libdebhelper-perl all 13.3.4 [189 kB] Get: 76 http://deb.debian.org/debian bullseye/main arm64 libtool all 2.4.6-15 [513 kB] Get: 77 http://deb.debian.org/debian bullseye/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 78 http://deb.debian.org/debian bullseye/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 79 http://deb.debian.org/debian bullseye/main arm64 libsub-override-perl all 0.09-2 [10.2 kB] Get: 80 http://deb.debian.org/debian bullseye/main arm64 libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB] Get: 81 http://deb.debian.org/debian bullseye/main arm64 dh-strip-nondeterminism all 1.11.0-1 [15.3 kB] Get: 82 http://deb.debian.org/debian bullseye/main arm64 libelf1 arm64 0.183-1 [164 kB] Get: 83 http://deb.debian.org/debian bullseye/main arm64 dwz arm64 0.13+20210201-1 [155 kB] Get: 84 http://deb.debian.org/debian bullseye/main arm64 libicu67 arm64 67.1-7 [8467 kB] Get: 85 http://deb.debian.org/debian bullseye/main arm64 libxml2 arm64 2.9.10+dfsg-6.7 [629 kB] Get: 86 http://deb.debian.org/debian bullseye/main arm64 gettext arm64 0.21-4 [1261 kB] Get: 87 http://deb.debian.org/debian bullseye/main arm64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 88 http://deb.debian.org/debian bullseye/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 89 http://deb.debian.org/debian bullseye/main arm64 debhelper all 13.3.4 [1049 kB] Get: 90 http://deb.debian.org/debian bullseye/main arm64 python3-lib2to3 all 3.9.2-1 [77.8 kB] Get: 91 http://deb.debian.org/debian bullseye/main arm64 python3-distutils all 3.9.2-1 [143 kB] Get: 92 http://deb.debian.org/debian bullseye/main arm64 dh-python all 4.20201102+nmu1 [99.4 kB] Get: 93 http://deb.debian.org/debian bullseye/main arm64 python3-pkg-resources all 52.0.0-4 [190 kB] Get: 94 http://deb.debian.org/debian bullseye/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2.1 [69.3 kB] Get: 95 http://deb.debian.org/debian bullseye/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2.1 [105 kB] Get: 96 http://deb.debian.org/debian bullseye/main arm64 libldap-2.4-2 arm64 2.4.57+dfsg-3 [222 kB] Get: 97 http://deb.debian.org/debian bullseye/main arm64 libnghttp2-14 arm64 1.43.0-1 [73.8 kB] Get: 98 http://deb.debian.org/debian bullseye/main arm64 libpsl5 arm64 0.21.0-1.2 [57.1 kB] Get: 99 http://deb.debian.org/debian bullseye/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 100 http://deb.debian.org/debian bullseye/main arm64 libssh2-1 arm64 1.9.0-2 [150 kB] Get: 101 http://deb.debian.org/debian bullseye/main arm64 libcurl3-gnutls arm64 7.74.0-1.3 [317 kB] Get: 102 http://deb.debian.org/debian bullseye/main arm64 libdeflate0 arm64 1.7-1 [47.7 kB] Get: 103 http://deb.debian.org/debian bullseye/main arm64 libhts3 arm64 1.11-4 [346 kB] Get: 104 http://deb.debian.org/debian bullseye/main arm64 libncurses6 arm64 6.2+20201114-2 [93.2 kB] Get: 105 http://deb.debian.org/debian bullseye/main arm64 samtools arm64 1.11-1 [526 kB] Get: 106 http://deb.debian.org/debian bullseye/main arm64 fastaq all 3.17.0-3 [47.8 kB] Get: 107 http://deb.debian.org/debian bullseye/main arm64 fonts-lyx all 2.3.6-1 [205 kB] Get: 108 http://deb.debian.org/debian bullseye/main arm64 help2man arm64 1.48.1 [190 kB] Get: 109 http://deb.debian.org/debian bullseye/main arm64 libblas3 arm64 3.9.0-3 [101 kB] Get: 110 http://deb.debian.org/debian bullseye/main arm64 libcapnp-0.7.0 arm64 0.7.0-7 [934 kB] Get: 111 http://deb.debian.org/debian bullseye/main arm64 libexpat1-dev arm64 2.2.10-2 [126 kB] Get: 112 http://deb.debian.org/debian bullseye/main arm64 libfml0 arm64 0.1+git20190320.b499514-1+b1 [65.9 kB] Get: 113 http://deb.debian.org/debian bullseye/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-2 [189 kB] Get: 114 http://deb.debian.org/debian bullseye/main arm64 libfml-dev arm64 0.1+git20190320.b499514-1+b1 [79.5 kB] Get: 115 http://deb.debian.org/debian bullseye/main arm64 libgfortran5 arm64 10.2.1-6 [333 kB] Get: 116 http://deb.debian.org/debian bullseye/main arm64 libgslcblas0 arm64 2.6+dfsg-2 [73.4 kB] Get: 117 http://deb.debian.org/debian bullseye/main arm64 libgsl25 arm64 2.6+dfsg-2 [812 kB] Get: 118 http://deb.debian.org/debian bullseye/main arm64 libimagequant0 arm64 2.12.2-1.1 [30.3 kB] Get: 119 http://deb.debian.org/debian bullseye/main arm64 libjbig0 arm64 2.1-3.1+b2 [27.8 kB] Get: 120 http://deb.debian.org/debian bullseye/main arm64 libjpeg62-turbo arm64 1:2.0.6-4 [133 kB] Get: 121 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get: 122 http://deb.debian.org/debian bullseye/main arm64 libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB] Get: 123 http://deb.debian.org/debian bullseye/main arm64 libjs-underscore all 1.9.1~dfsg-3 [100 kB] Get: 124 http://deb.debian.org/debian bullseye/main arm64 libjs-sphinxdoc all 3.4.3-2 [127 kB] Get: 125 http://deb.debian.org/debian bullseye/main arm64 liblapack3 arm64 3.9.0-3 [1541 kB] Get: 126 http://deb.debian.org/debian bullseye/main arm64 liblcms2-2 arm64 2.12~rc1-2 [140 kB] Get: 127 http://deb.debian.org/debian bullseye/main arm64 libminimap0 arm64 0.2-5 [21.1 kB] Get: 128 http://deb.debian.org/debian bullseye/main arm64 libminimap-dev arm64 0.2-5 [32.7 kB] Get: 129 http://deb.debian.org/debian bullseye/main arm64 libmurmurhash2 arm64 1.5-2 [6028 B] Get: 130 http://deb.debian.org/debian bullseye/main arm64 libpython3.9 arm64 3.9.2-1 [1556 kB] Get: 131 http://deb.debian.org/debian bullseye/main arm64 libpython3.9-dev arm64 3.9.2-1 [3835 kB] Get: 132 http://deb.debian.org/debian bullseye/main arm64 libpython3-dev arm64 3.9.2-3 [21.7 kB] Get: 133 http://deb.debian.org/debian bullseye/main arm64 libpython3-all-dev arm64 3.9.2-3 [1068 B] Get: 134 http://deb.debian.org/debian bullseye/main arm64 libwebp6 arm64 0.6.1-2.1 [244 kB] Get: 135 http://deb.debian.org/debian bullseye/main arm64 libtiff5 arm64 4.2.0-1 [276 kB] Get: 136 http://deb.debian.org/debian bullseye/main arm64 libwebpdemux2 arm64 0.6.1-2.1 [87.5 kB] Get: 137 http://deb.debian.org/debian bullseye/main arm64 libwebpmux3 arm64 0.6.1-2.1 [96.7 kB] Get: 138 http://deb.debian.org/debian bullseye/main arm64 mash arm64 2.2.2+dfsg-2 [134 kB] Get: 139 http://deb.debian.org/debian bullseye/main arm64 mummer arm64 3.23+dfsg-7 [640 kB] Get: 140 http://deb.debian.org/debian bullseye/main arm64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get: 141 http://deb.debian.org/debian bullseye/main arm64 python3-all arm64 3.9.2-3 [1056 B] Get: 142 http://deb.debian.org/debian bullseye/main arm64 python3.9-dev arm64 3.9.2-1 [515 kB] Get: 143 http://deb.debian.org/debian bullseye/main arm64 python3-dev arm64 3.9.2-3 [24.8 kB] Get: 144 http://deb.debian.org/debian bullseye/main arm64 python3-all-dev arm64 3.9.2-3 [1064 B] Get: 145 http://deb.debian.org/debian bullseye/main arm64 python3-numpy arm64 1:1.19.5-1 [3196 kB] Get: 146 http://deb.debian.org/debian bullseye/main arm64 python3-reportlab-accel arm64 3.5.59-1 [38.6 kB] Get: 147 http://deb.debian.org/debian bullseye/main arm64 python3-pil arm64 8.1.2+dfsg-0.2 [428 kB] Get: 148 http://deb.debian.org/debian bullseye/main arm64 python3-reportlab all 3.5.59-1 [575 kB] Get: 149 http://deb.debian.org/debian bullseye/main arm64 python3-biopython arm64 1.78+dfsg-4 [1389 kB] Get: 150 http://deb.debian.org/debian bullseye/main arm64 python3-soupsieve all 2.2.1-1 [34.7 kB] Get: 151 http://deb.debian.org/debian bullseye/main arm64 python3-bs4 all 4.9.3-1 [112 kB] Get: 152 http://deb.debian.org/debian bullseye/main arm64 python3-six all 1.16.0-1 [17.1 kB] Get: 153 http://deb.debian.org/debian bullseye/main arm64 python3-cycler all 0.10.0-3 [8084 B] Get: 154 http://deb.debian.org/debian bullseye/main arm64 python3-dateutil all 2.8.1-5 [81.7 kB] Get: 155 http://deb.debian.org/debian bullseye/main arm64 python3-dendropy all 4.5.1-1 [273 kB] Get: 156 http://deb.debian.org/debian bullseye/main arm64 python3-kiwisolver arm64 1.3.1-1+b1 [51.6 kB] Get: 157 http://deb.debian.org/debian bullseye/main arm64 python3-pyparsing all 2.4.7-1 [109 kB] Get: 158 http://deb.debian.org/debian bullseye/main arm64 python3-matplotlib arm64 3.3.4-1 [4109 kB] Get: 159 http://deb.debian.org/debian bullseye/main arm64 python3-nose all 1.3.7-7 [133 kB] Get: 160 http://deb.debian.org/debian bullseye/main arm64 python3-pymummer all 0.11.0-2 [11.3 kB] Get: 161 http://deb.debian.org/debian bullseye/main arm64 python3-pysam arm64 0.15.4+ds-3+b2 [1386 kB] Get: 162 http://deb.debian.org/debian bullseye/main arm64 python3-setuptools all 52.0.0-4 [366 kB] Get: 163 http://deb.debian.org/debian bullseye/main arm64 python3-tk arm64 3.9.2-1 [100 kB] Fetched 70.8 MB in 1s (53.4 MB/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 ... 19646 files and directories currently installed.) Preparing to unpack .../0-bsdextrautils_2.36.1-7_arm64.deb ... Unpacking bsdextrautils (2.36.1-7) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../1-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-6_arm64.deb ... Unpacking groff-base (1.22.4-6) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../3-libpipeline1_1.5.3-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.3-1) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.4-2_arm64.deb ... Unpacking man-db (2.9.4-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../5-readline-common_8.1-1_all.deb ... Unpacking readline-common (8.1-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../6-libreadline8_8.1-1_arm64.deb ... Unpacking libreadline8:arm64 (8.1-1) ... Selecting previously unselected package libsigsegv2:arm64. Preparing to unpack .../7-libsigsegv2_2.13-1_arm64.deb ... Unpacking libsigsegv2:arm64 (2.13-1) ... Setting up readline-common (8.1-1) ... Setting up libreadline8:arm64 (8.1-1) ... Setting up libsigsegv2:arm64 (2.13-1) ... Selecting previously unselected package gawk. (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 ... 20252 files and directories currently installed.) Preparing to unpack .../gawk_1%3a5.1.0-1_arm64.deb ... Unpacking gawk (1:5.1.0-1) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../liblocale-gettext-perl_1.07-4+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4+b1) ... Selecting previously unselected package libpython3.9-minimal:arm64. Preparing to unpack .../libpython3.9-minimal_3.9.2-1_arm64.deb ... Unpacking libpython3.9-minimal:arm64 (3.9.2-1) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.2.10-2_arm64.deb ... Unpacking libexpat1:arm64 (2.2.10-2) ... Selecting previously unselected package python3.9-minimal. Preparing to unpack .../python3.9-minimal_3.9.2-1_arm64.deb ... Unpacking python3.9-minimal (3.9.2-1) ... Setting up libpython3.9-minimal:arm64 (3.9.2-1) ... Setting up libexpat1:arm64 (2.2.10-2) ... Setting up python3.9-minimal (3.9.2-1) ... Selecting previously unselected package python3-minimal. (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 ... 20736 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.9.2-3_arm64.deb ... Unpacking python3-minimal (3.9.2-3) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_4.0.0_all.deb ... Unpacking media-types (4.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.69_all.deb ... Unpacking mailcap (3.69) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package libmpdec3:arm64. Preparing to unpack .../4-libmpdec3_2.5.1-1_arm64.deb ... Unpacking libmpdec3:arm64 (2.5.1-1) ... Selecting previously unselected package libpython3.9-stdlib:arm64. Preparing to unpack .../5-libpython3.9-stdlib_3.9.2-1_arm64.deb ... Unpacking libpython3.9-stdlib:arm64 (3.9.2-1) ... Selecting previously unselected package python3.9. Preparing to unpack .../6-python3.9_3.9.2-1_arm64.deb ... Unpacking python3.9 (3.9.2-1) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../7-libpython3-stdlib_3.9.2-3_arm64.deb ... Unpacking libpython3-stdlib:arm64 (3.9.2-3) ... Setting up python3-minimal (3.9.2-3) ... Selecting previously unselected package python3. (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 ... 21157 files and directories currently installed.) Preparing to unpack .../000-python3_3.9.2-3_arm64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_1.1.1k-1_arm64.deb ... Unpacking openssl (1.1.1k-1) ... 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Selecting previously unselected package python3-numpy. Preparing to unpack .../123-python3-numpy_1%3a1.19.5-1_arm64.deb ... Unpacking python3-numpy (1:1.19.5-1) ... Selecting previously unselected package python3-reportlab-accel:arm64. Preparing to unpack .../124-python3-reportlab-accel_3.5.59-1_arm64.deb ... Unpacking python3-reportlab-accel:arm64 (3.5.59-1) ... Selecting previously unselected package python3-pil:arm64. Preparing to unpack .../125-python3-pil_8.1.2+dfsg-0.2_arm64.deb ... Unpacking python3-pil:arm64 (8.1.2+dfsg-0.2) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../126-python3-reportlab_3.5.59-1_all.deb ... Unpacking python3-reportlab (3.5.59-1) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../127-python3-biopython_1.78+dfsg-4_arm64.deb ... Unpacking python3-biopython (1.78+dfsg-4) ... Selecting previously unselected package python3-soupsieve. 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Preparing to unpack .../134-python3-kiwisolver_1.3.1-1+b1_arm64.deb ... Unpacking python3-kiwisolver (1.3.1-1+b1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../135-python3-pyparsing_2.4.7-1_all.deb ... Unpacking python3-pyparsing (2.4.7-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../136-python3-matplotlib_3.3.4-1_arm64.deb ... Unpacking python3-matplotlib (3.3.4-1) ... Selecting previously unselected package python3-nose. Preparing to unpack .../137-python3-nose_1.3.7-7_all.deb ... Unpacking python3-nose (1.3.7-7) ... Selecting previously unselected package python3-pymummer. Preparing to unpack .../138-python3-pymummer_0.11.0-2_all.deb ... Unpacking python3-pymummer (0.11.0-2) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../139-python3-pysam_0.15.4+ds-3+b2_arm64.deb ... Unpacking python3-pysam (0.15.4+ds-3+b2) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../140-python3-setuptools_52.0.0-4_all.deb ... Unpacking python3-setuptools (52.0.0-4) ... Selecting previously unselected package python3-tk:arm64. Preparing to unpack .../141-python3-tk_3.9.2-1_arm64.deb ... Unpacking python3-tk:arm64 (3.9.2-1) ... Setting up cd-hit (4.8.1-3) ... Setting up media-types (4.0.0) ... Setting up libpipeline1:arm64 (1.5.3-1) ... Setting up liblcms2-2:arm64 (2.12~rc1-2) ... Setting up libxau6:arm64 (1:1.0.9-1) ... Setting up libpsl5:arm64 (0.21.0-1.2) ... Setting up ttf-bitstream-vera (1.10-8.1) ... Setting up bsdextrautils (2.36.1-7) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:arm64 (67.1-7) ... Setting up libgslcblas0:arm64 (2.6+dfsg-2) ... Setting up libmurmurhash2:arm64 (1.5-2) ... Setting up ruby-power-assert (1.1.7-2) ... Setting up libmagic-mgc (1:5.39-3) ... Setting up libgsl25:arm64 (2.6+dfsg-2) ... Setting up gawk (1:5.1.0-1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:arm64 (0.2.2-1) ... Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.3.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b2) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libnghttp2-14:arm64 (1.43.0-1) ... Setting up libmagic1:arm64 (1:5.39-3) ... Setting up libdeflate0:arm64 (1.7-1) ... Setting up gettext-base (0.21-4) ... Setting up m4 (1.4.18-5) ... Setting up file (1:5.39-3) ... Setting up libcapnp-0.7.0:arm64 (0.7.0-7) ... Setting up libfml0:arm64 (0.1+git20190320.b499514-1+b1) ... Setting up libjbig0:arm64 (2.1-3.1+b2) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2.1) ... Setting up ruby-minitest (5.13.0-1) ... Setting up libminimap0 (0.2-5) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.2.10-2) ... Setting up libjpeg62-turbo:arm64 (1:2.0.6-4) ... Setting up ruby-test-unit (3.3.9-1) ... Setting up libx11-data (2:1.7.1-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:arm64 (6.2+20201114-2) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libimagequant0:arm64 (2.12.2-1.1) ... Setting up libpng16-16:arm64 (1.6.37-3) ... Setting up mash (2.2.2+dfsg-2) ... Setting up libtcl8.6:arm64 (8.6.11+dfsg-1) ... Setting up autopoint (0.21-4) ... Setting up libwebp6:arm64 (0.6.1-2.1) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:arm64 (10.2.1-6) ... Setting up autoconf (2.69-14) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-2) ... Setting up libmd0:arm64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up libmpdec3:arm64 (2.5.1-1) ... Setting up mummer (3.23+dfsg-7) ... Setting up libsub-override-perl (0.09-2) ... Setting up libssh2-1:arm64 (1.9.0-2) ... Setting up libtiff5:arm64 (4.2.0-1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up openssl (1.1.1k-1) ... Setting up libwebpmux3:arm64 (0.6.1-2.1) ... Setting up libbsd0:arm64 (0.11.3-1) ... Setting up mailcap (3.69) ... Setting up libelf1:arm64 (0.183-1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:arm64 (2.9.10+dfsg-6.7) ... Setting up liblocale-gettext-perl (1.07-4+b1) ... Setting up libpython3.9-stdlib:arm64 (3.9.2-1) ... Setting up libpython3-stdlib:arm64 (3.9.2-3) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up automake (1:1.16.3-2) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.11.0-1) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up liblapack3:arm64 (3.9.0-3) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.14-3) ... Setting up gettext (0.21-4) ... Setting up libfml-dev:arm64 (0.1+git20190320.b499514-1+b1) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15) ... Setting up libwebpdemux2:arm64 (0.6.1-2.1) ... Setting up libedit2:arm64 (3.1-20191231-2+b1) ... Setting up libldap-2.4-2:arm64 (2.4.57+dfsg-3) ... Setting up libcurl3-gnutls:arm64 (7.74.0-1.3) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up help2man (1.48.1) ... Setting up dh-autoreconf (20) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libpython3.9:arm64 (3.9.2-1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-8) ... Setting up libfreetype6:arm64 (2.10.4+dfsg-1) ... Setting up ucf (3.0043) ... Setting up libminimap-dev (0.2-5) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up dh-strip-nondeterminism (1.11.0-1) ... Setting up dwz (0.13+20210201-1) ... Setting up groff-base (1.22.4-6) ... Setting up libx11-6:arm64 (2:1.7.1-1) ... Setting up python3.9 (3.9.2-1) ... Setting up libhts3:arm64 (1.11-4) ... Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libxext6:arm64 (2:1.3.3-1.1) ... Setting up libpython3.9-dev:arm64 (3.9.2-1) ... Setting up python3 (3.9.2-3) ... Setting up rubygems-integration (1.18) ... Setting up man-db (2.9.4-2) ... Not building database; man-db/auto-update is not 'true'. Setting up samtools (1.11-1) ... Setting up bowtie2 (2.4.2-2+b3) ... Setting up python3-six (1.16.0-1) ... Setting up python3-pil:arm64 (8.1.2+dfsg-0.2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:arm64 (3.5.59-1) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-reportlab (3.5.59-1) ... Setting up python3.9-dev (3.9.2-1) ... Setting up python3-dateutil (2.8.1-5) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libfontconfig1:arm64 (2.13.1-4.2) ... Setting up python3-lib2to3 (3.9.2-1) ... Setting up python3-soupsieve (2.2.1-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-distutils (3.9.2-1) ... Setting up dh-python (4.20201102+nmu1) ... Setting up libxft2:arm64 (2.3.2-2) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up libpython3-dev:arm64 (3.9.2-3) ... Setting up python3-setuptools (52.0.0-4) ... Setting up libtk8.6:arm64 (8.6.11-2) ... Setting up fastaq (3.17.0-3) ... Setting up python3-all (3.9.2-3) ... Setting up debhelper (13.3.4) ... Setting up python3-nose (1.3.7-7) ... Setting up python3-bs4 (4.9.3-1) ... Setting up python3-pymummer (0.11.0-2) ... Setting up libpython3-all-dev:arm64 (3.9.2-3) ... Setting up python3-dev (3.9.2-3) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-biopython (1.78+dfsg-4) ... Setting up python3-dendropy (4.5.1-1) ... Setting up python3-all-dev (3.9.2-3) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-tk:arm64 (3.9.2-1) ... Setting up rake (13.0.3-1) ... Setting up ruby-rubygems (3.2.5-2) ... Setting up libruby2.7:arm64 (2.7.3-2) ... Setting up ruby2.7 (2.7.3-2) ... Setting up ruby (1:2.7+2) ... Setting up ruby-asciidoctor (2.0.12-2) ... Setting up asciidoctor (2.0.12-2) ... Processing triggers for libc-bin (2.31-12) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.25.3-1.1). 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 arm64 libnumber-compare-perl all 0.03-1.1 [6956 B] Get:2 http://deb.debian.org/debian bullseye/main arm64 libtext-glob-perl all 0.11-1 [8888 B] Get:3 http://deb.debian.org/debian bullseye/main arm64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:4 http://deb.debian.org/debian bullseye/main arm64 usrmerge all 25 [13.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 59.5 kB in 0s (2178 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 ... 30141 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 hostname: Temporary failure in name resolution I: Running cd /build/ariba-2.14.6+ds/ && 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 > ../ariba_2.14.6+ds-1_source.changes dpkg-buildpackage: info: source package ariba dpkg-buildpackage: info: source version 2.14.6+ds-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Sascha Steinbiss dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/ariba-2.14.6+ds' rm -rf /build/ariba-2.14.6+ds/debian/man dh_auto_clean -- I: pybuild base:232: python3.9 setup.py clean running clean removing '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build' (and everything under it) 'build/bdist.linux-arm64' does not exist -- can't clean it 'build/scripts-3.9' does not exist -- can't clean it make[1]: Leaving directory '/build/ariba-2.14.6+ds' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:232: python3.9 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py build running build running build_py creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/assembly.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/assembly_variants.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/reference_data.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/__init__.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/sequence_metadata.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/versions.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/clusters.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/ref_preparer.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/cluster.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/aln_to_metadata.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/mapping.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/ref_genes_getter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/cdhit.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/common.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/faidx.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/mic_plotter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/summary_sample.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/histogram.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/report.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/sequence_variant.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/pubmlst_getter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/read_store.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/tb.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/report_filter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/flag.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/external_progs.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/link.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/summary_cluster_variant.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/samtools_variants.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/mlst_reporter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/megares_zip_parser.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/summary.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/megares_data_finder.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/bam_parse.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/read_filter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/pubmlst_ref_preparer.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/mlst_profile.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/assembly_compare.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/scaffold_graph.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/report_flag_expander.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/vfdb_parser.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/summary_cluster.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/card_record.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/refdata_query.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba copying ariba/ref_seq_chooser.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/aln2meta.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/getref.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/__init__.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/pubmlstspecies.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/pubmlstget.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/refquery.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/reportfilter.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/prepareref_tb.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/micplot.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/flag.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/summary.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/run.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/prepareref.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/version.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks copying ariba/tasks/expandflag.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/assembly_variants_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/ncbi_getter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/mapping_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/common_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/__init__.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/scaffold_graph_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/megares_data_finder_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/cluster_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/cdhit_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/ref_seq_chooser_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/megares_zip_parser_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/versions_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/card_record_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/assembly_compare_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/test_refdata_query.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/summary_cluster_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/mlst_profile_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/summary_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/clusters_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/samtools_variants_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/ref_preparer_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/bam_parse_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/external_progs_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/ref_genes_getter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/histogram_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/faidx_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/link_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/flag_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/tb_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/summary_cluster_variant_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/pubmlst_getter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/sequence_metadata_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/sequence_variant_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/assembly_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/aln_to_metadata_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/read_filter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/mlst_reporter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/report_filter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/summary_sample_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/mic_plotter_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/report_flag_expander_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/read_store_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/reference_data_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/vfdb_parser_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests copying ariba/tests/pubmlst_ref_preparer_test.py -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_seqs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data copying ariba/test_run_data/metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.fa.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.gb -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_ok.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_write_report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_init.fofn -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_fasta_file.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_good.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.read_store -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.3 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_rename_sequences.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.params.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.out -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_getter.dbases.xml -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_data_info_file -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.out.csv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_fofn -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.out.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.rename -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_rename_file.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_short.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.expected.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_long.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_clean.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/dummy.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.1.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.profile.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_bad.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding copying ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding copying ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only copying ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only copying ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 creating /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene running build_ext building 'minimap_ariba' extension creating build creating build/temp.linux-arm64-3.9 creating build/temp.linux-arm64-3.9/ariba creating build/temp.linux-arm64-3.9/ariba/ext aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.9 -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-arm64-3.9/ariba/ext/minimap_ariba.o ariba/ext/minimap_ariba.cpp: In function 'bool readMappingOk(const mm_reg1_t*, const mm_idx_t*, const kseq_t*, uint32_t)': ariba/ext/minimap_ariba.cpp:371:23: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare] 371 | if (r->qe - r->qs < std::min((unsigned) 50, (int) 0.5 * ks->seq.l)) | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:381:26: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 381 | startOk = (r->qs < endTolerance || refLength - r->re < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:382:60: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 382 | endOk = (ks->seq.l - r->qe < endTolerance || r->rs < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:26: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 386 | startOk = (r->qs < endTolerance || r->rs < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ ariba/ext/minimap_ariba.cpp:386:50: warning: comparison of integer expressions of different signedness: 'const int32_t' {aka 'const int'} and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] 386 | startOk = (r->qs < endTolerance || r->rs < endTolerance); | ~~~~~~^~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.9/ariba/ext/minimap_ariba.o -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/minimap_ariba.cpython-39-aarch64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-arm64-3.9/ariba/ext/fml-asm_ariba.o aarch64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.9/ariba/ext/fml-asm_ariba.o -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/fermilite_ariba.cpython-39-aarch64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/build/python3.9-PN012d/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.9 -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-arm64-3.9/ariba/ext/vcfcall_ariba.o aarch64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/build/ariba-2.14.6+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-arm64-3.9/ariba/ext/vcfcall_ariba.o -o /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/vcfcall_ariba.cpython-39-aarch64-linux-gnu.so running build_scripts creating build/scripts-3.9 copying and adjusting scripts/ariba -> build/scripts-3.9 changing mode of build/scripts-3.9/ariba from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:232: cd /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build; python3.9 -m nose -v WARNING: spades not found in path. Looked for spades.py test _check_coding_seq ... ok test _check_insertion_coords ... ok test _check_seq_lengths_same ... ok test _check_sequences with coding seqs ... ok test _check_sequences with noncoding seqs ... ok test _check_variants_match_sequences ... ok test _insertion_coords ... ok test _load_aln_file ... ok test _load_vars_file bad input files ... ok test _load_vars_file good input file ... ok test _make_cluster_file ... ok test _make_unpadded_insertion_coords ... ok test _make_unpadded_seqs ... ok test _padded_to_unpadded_nt_position ... ok test run coding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant A2D (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq2 ok test run noncoding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant C5T (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq2 ok test _unpadded_to_padded_nt_position ... ok test variant_ids_are_unique ... ok test _variants_to_tsv_lines coding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant A2D (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant F2E (id2) in sequence seq5 ... Ignoring for seq2 ok test _variants_to_tsv_lines noncoding sequences ... Warning: position has a gap in sequence seq3 corresponding to variant C5T (id1) in sequence seq1 ... Ignoring for seq3 Warning: position has a gap in sequence seq1 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq1 Warning: position has a gap in sequence seq2 corresponding to variant A5T (id2) in sequence seq5 ... Ignoring for seq2 ok test _find_next_stop_codon ... ok test _find_previous_start_codon ... ok test _gene_from_nucmer_match ... ok test _get_assembled_reference_sequences ... ok test _get_gene_matching_ref ... ok test _longest_nucmer_hit_in_ref ... ok test nucmer_hit_containing_reference_position ... ok test _nucmer_hits_to_assembly_coords ... ok test _nucmer_hits_to_percent_identity ... ok test _nucmer_hits_to_ref_and_qry_coords ... ok test nucmer_hits_to_ref_coords ... ok test _parse_nucmer_coords_file ... ok test ref_cov_per_contig ... ok test _ref_covered_by_at_least_one_full_length_contig ... ok test _ref_has_region_assembled_twice ... ok test _whole_gene_covered_by_nucmer_hits ... ok test _assemble_with_fermilite ... ok test _assemble_with_fermilite fails ... ok test _assemble_with_spades ... SKIP: Spades assembler is optional and is not configured test _assemble_with_spades handles spades fail ... SKIP: Spades assembler is optional and is not configured test _check_spades_log_file ... Error running SPAdes. Cannot continue. This is the error from the log file /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.bad ... == Error == system call for: "['/foo/bar/SPAdes-3.6.0-Linux/bin/spades', '/spam/eggs/K21/configs/config.info']" finished abnormally, err code: -7 ok test _fix_contig_orientation ... ok test _parse_bam ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam' ok test _run_fermilite ... ok test _run_fermilite when it fails ... ok test filter_mummer_variants ... ok test _get_codon_start ... ok test _get_mummer_variants when there are variants ... ok test _get_mummer_variants when no variants ... ok test _get_remaining_known_ref_variants with amino acids ... ok test _get_remaining_known_ref_variants with nucleotides ... ok test _get_variant_effect ... ok test get_variants presence absence genes ... ok test get_variants variants only ... ok test _get_one_variant_for_one_contig_coding ... ok test _get_one_variant_for_one_contig_non_coding ... ok test parse ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.bam' ok test _sam_to_soft_clipped ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam' ok test _update_soft_clipped_from_sam ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam' ok test _update_unmapped_mates_from_sam ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam' [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam' ok test _write_soft_clipped_to_file ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/dummy.bam' ok test _write_unmapped_mates_to_file ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/dummy.bam' ok test _ARO_accession ... ok test _ARO_description ... ok test _ARO_id ... ok test _ARO_name ... ok test _ARO_name_to_fasta_name ... ok test _dna_seqs_and_genbank_ids ... Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo Missing data from foo ok test_get_data (ariba.tests.card_record_test.TestCardRecord) ... ok test snps ... ok test fake_run ... ok test fake_run min_cluster 42 ... ok test fake_run with non-unique names ... ok test _get_clusters_from_bak_file ... ok test_get_run_cmd_with_default_memory ... ok test_get_run_cmd_with_non_default_memory ... ok test_get_run_cmd_with_unlimited_memory ... ok test init_fail_infile_missing ... ok test_init_fail_invalid_memory ... ok test _load_user_clusters_file with bad input files ... ok test _load_user_clusters_file with good input file ... WARNING: ignoring sequence seq6 from clusters file because not in fasta file. This probably means it failed sanity checks - see the log files 01.filter.check_genes.log, 01.filter.check_metadata.log. ok test _load_user_clusters_file with good input file with some renamed ... ok test run ... ok test run_get_clusters_from_file ... ok test run_get_clusters_from_file with renaming ... ok test run with min_cluster_number 42 ... ok test complete run of cluster when assembly fails ... ok test complete run of cluster when choosing ref seq fails ... ok test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample has the var ... ok Test complete run where there is a deleted codon ... ok Test complete run where there is a inserted codon ... ok test complete run where samtools calls a snp at a known snp location in a presence/absence gene ... ok test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding ... ok Test complete run where there is a codon with a SNP and an indel ... ok test complete run of cluster when filtering removes all reads ... ok test complete run where gene extended because too different at end for full nucmer match ... ok test complete run of cluster on a noncoding sequence ... ok test complete run of cluster on a presence absence gene ... ok test complete run of cluster on a variants only gene when variant is present ... ok test complete run of cluster on a variants only gene when variant not present ... ok test complete run of cluster on a variants only gene when variant not present but always report variant ... ok Test complete run where only part of the ref gene is present in the reads ... ok test complete run of cluster when nearest ref is outside cluster ... ok test complete run where samtools calls a snp in a presence/absence noncoding sequence at a known snp position ... ok test complete run where samtools calls a snp in a presence/absence gene ... ok test complete run where samtools calls a snp in a presence/absence noncoding sequence ... ok test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does have variant ... ok test complete run where samtools calls a snp in a variant only gene ... ok test complete run where samtools calls a snp at a known snp location in a variant only gene, gene does not have variant ... ok test complete run where samtools calls a snp in a presence/absence noncoding sequence ... ok test complete run where samtools calls a snp at a known snp location in a presence/absence noncoding and sample does not have the var ... ok test init_fail_files_missing ... ok Test _make_reads_for_assembly when sampling from reads ... ok Test _make_reads_for_assembly when just makes symlinks ... ok Test _number_of_reads_for_assembly ... ok test _write_catted_genes_matching_refs_fasta ... ok test _load_minimap_files ... ok test _load_minimap_insert_histogram ... ok test _load_minimap_out_cluster2representative ... ok test _load_minimap_out_cluster_counts ... ok test _load_minimap_proper_pairs ... ok test _load_reference_data_from_dir ... ok test _load_reference_data_info_file ... ok test test_minimap_reads_to_all_ref_seqs ... ok test complete run with TB amr calling ... ok test _set_insert_size_data ... ok test _write_catted_assembled_seqs_fasta ... ok test _write_catted_assemblies_fasta ... ok test _write_mlst_reports ... ok test_write_report (ariba.tests.clusters_test.TestClusters) ... ok test _write_tb_resistance_calls_json ... ok test cat_files ... ok test rmtree ... ok Test that external programs are found ... ok test write_fa_subset ... ok Test add ... ok Test has ... ok Test __init__ and to_number ... ok Test set_flag ... ok Test __str__ ... ok Test to_comma_separated_string ... ok Test to_long_str ... ok Test add ... ok Test __len__ ... ok Test stats ... ok Test _to_bin ... ok test _distance_to_contig_end ... ok test _distance_to_contig_ends ... ok test link __init__ no links made ... ok test link __init__ link made ... ok test insert_size ... ok test __lt__ ... ok test merge ... ok test sort ... ok test _swap ... ok test bowtie2_index ... ok Test get_total_alignment_score ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam' ok Test run_bowtie2 unsorted ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bowtie2.bam' ok Test run_bowtie2 sorted ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam' ok Test run_bowtie2 unsorted remove both unmapped ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam' [E::idx_find_and_load] Could not retrieve index file for 'tmp.out.bowtie2_remove_both_unmapped.bam' ok test sam_pair_to_insert ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam' ok test sam_to_fastq ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam' ok test _get_url_for_version ... ok test _zips_from_index_page_string ... ok test _extract_files when all ok ... ok test _extract_files when one missing ... ok test _load_annotations_file ... ok test _load_header_mappings_file ... ok test _write_files ... WARNING: sequence "Only_in_fasta_file" has no record in annotations file WARNING: sequence "Only_in_fasta_file" has no record in header mappings file ok test _bottom_scatter_data ... ok test _filter_top_plot_data ... ok test _get_colours ... ok Test _get_top_plot_data ... ok Test _load_mic_file ... ok Test _load_summary_file ... ok Test _mic_string_to_float ... ok test _ordered_bottom_plot_rows ... ok test _ordered_colunns ... ok test _top_plot_scatter_counts ... ok test _top_plot_scatter_data ... ok test _top_plot_violin_data ... ok test _top_plot_y_ticks ... ok Test get_sequence_type ... ok Test has_gene ... ok test init ... WARNING: Same profile found twice in input file, but two different STs. Going to use the ST with the smaller number (2) ... STs are 2 3 and alleles are nusA:1, rpoB:26, eno:2, gltB:4, lepA:59, nuoL:2, nrdA:5 ok test init ... ok test when all alleles 100% there no variants ... ok test when one gene has a het snp ... ok test when one gene has two het snps ... ok test when allele combination is new ... ok test when one gene missing ... ok test _get_profile_and_fasta_urls ... ok test _get_species_list ... ok test _rename_seqs_in_fasta ... ok test _filter_seq_dict ... WARNING: Median sequence length is 5 but seq1 has length 1 which is too long or short. Removing. WARNING: Median sequence length is 5 but seq5 has length 14 which is too long or short. Removing. ok test _load_fasta_files_and_write_clusters_file ... WARNING: spades not found in path. Looked for spades.py ok test _cdhit_clstr_to_reads ... ok Test clean ... ok Test _compress_and_index_file ... ok Test get_reads fasta pair ... ok Test get_reads fastq interleaved ... ok Test get_reads fastq pair ... ok Test get_reads subset ... ok test _sort_file ... ok test _fix_virulencefinder_fasta_file ... WARNING: found line with ">" not at the start! Fixing. Line:AC>seq3 in file /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa WARNING: found line with ">" at the end! Fixing. Line:AACGT> in file /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa ok test _fasta_to_metadata ... ok test _rename_clusters ... ok test run ... WARNING. 1 sequence(s) excluded. Please see the 01.filter.check_genes.log and 01.filter.check_noncoding.log for details. This will show them: grep REMOVE tmp.ref_preparer_test_run/01.filter.check_genes.log cat tmp.ref_preparer_test_run/01.filter.check_noncoding.log WARNING. Problem with at least one variant. Problem variants are removed. Please see the file tmp.ref_preparer_test_run/01.filter.check_metadata.log for details. ok test run with no metadata input, all sequences are noncoding ... ok test run with noncoding sequences that are outside of the allowed size range ... WARNING. 5 sequence(s) excluded. Please see the 01.filter.check_genes.log and 01.filter.check_noncoding.log for details. This will show them: grep REMOVE tmp.ref_preparer_test_run_noncoding_checks/01.filter.check_genes.log cat tmp.ref_preparer_test_run_noncoding_checks/01.filter.check_noncoding.log WARNING. Problem with at least one variant. Problem variants are removed. Please see the file tmp.ref_preparer_test_run_noncoding_checks/01.filter.check_metadata.log for details. ok test _make_matching_contig_pieces_fasta ... ok Test full run where the best match is in the cluster ... ok Test full run where there is a match in cluster, but better match to seq not in cluster ... ok Test full run where ref seq completely contains another seq outside cluster ... ok Test full run where amount of flanking seq varies ... ok Test full run when nearest match is not in the cluster ... ok Test full run when there is nearest match in cluster, but no nucmer matches ... ok Test all_non_wild_type_variants ... ok Test _check_noncoding_seq ... ok Test cluster_with_cd_hit clusters from file ... ok Test cluster_with_cd_hit do not run cdhit ... ok Test cluster_with_cd_hit ... ok Test _filter_bad_variant_data ... WARNING: sequence "non_coding_not_in_fasta" found in metadata, but not in fasta file. Ignoring it. WARNING: sequence "presence_absence_not_in_fasta" found in metadata, but not in fasta file. Ignoring it. WARNING: sequence "variants_only_not_in_fasta" found in metadata, but not in fasta file. Ignoring it. ok Test __init__ fails when it should ... ok Test init with good input ... ok Test _load_all_fasta_files ... ok Test _load_all_metadata_tsvs ... ok Test _load_fasta_file ... ok Test _load_input_files_and_check_seq_names with bad input ... ok Test _load_input_files_and_check_seq_names with good input ... WARNING: sequence "seq3" found in metadata, but not in fasta file. Ignoring it. ok Test _load_metadata_tsv ... ok Test _load_rename_file ... ok Test _new_seq_name ... ok Test _remove_bad_genes ... ok Test _remove_bad_noncoding_seqs ... ok Test _rename_metadata_set ... ok Test _rename_names_in_metadata ... ok Test _rename_names_in_seq_dict ... ok Test rename_sequences ... ok Test _seq_names_to_rename_dict ... ok Test sequence ... ok Test sequence_type ... ok Test _try_to_get_gene_seq ... ok Test write_cluster_allocation_file ... ok Test _write_metadata_tsv ... ok Test write_seqs_to_fasta ... ok Test _write_sequences_to_files ... ok Test _dict_to_report_line ... ok Test _filter_dicts ... ok Test _filter_list_of_dicts where all fail ... ok Test _filter_list_of_dicts with an essential line but all others fail ... ok Test _filter_list_of_dicts with a line that passes ... ok Test _flag_passes_filter ... ok test __init__ on bad input file ... ok test __init__ on good input file ... ok test_load_report (ariba.tests.report_filter_test.TestReportFilter) ... ok Test _remove_all_after_first_frameshift ... ok Test _remove_all_after_first_frameshift when gene is complete ... ok Test _report_dict_passes_essential_filters ... ok Test _report_dict_passes_non_essential_filters with known vars ... ok Test _report_dict_passes_non_essential_filters with synonymous AA changes ... ok test_report_line_to_dict (ariba.tests.report_filter_test.TestReportFilter) ... ok Test run ... ok Test write_report_tsv ... ok test run ... ok test get_depths_at_position ... ok test _get_read_depths ... ok test _get_variant_positions_from_vcf ... ok test _get_variants ... ok test _make_vcf_and_read_depths_files ... ok test total_depth_per_contig ... ok test variants_in_coords ... ok test _contig_graph_is_consistent ... ok test _make_graph ... ok test _remove_low_cov_links ... ok test update_from_sam ... [E::idx_find_and_load] Could not retrieve index file for '/build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam' ok test write_all_links_to_file ... ok test has_variant ... ok Test init fails on bad lines ... ok test init ok on good input ... ok test __str__ ... ok test to_string ... ok test has_variant ... ok Test init fails on bad variant strings ... ok Test init ok ... ok Test init ok and str ... ok test nucleotide_range ... ok test sanity_check_against_seq with translate False ... ok test sanity_check_against_seq with translate True ... ok Test add_data_dict ... ok Test column_summary_data ... ok test gather_data ... ok test _get_all_nonsynon_variants_set ... ok Test _get_known_noncoding_het_snp ... ok Test _get_nonsynonymous_var ... ok test_has_any_known_variant (ariba.tests.summary_cluster_test.TestSummaryCluster) ... ok Test _has_any_nonsynonymous ... ok Test _has_any_novel_nonsynonymous ... ok Test _has_any_part_of_ref_assembled ... ok Test _has_known_variant ... ok Test _has_match ... ok Test _has_nonsynonymous ... ok Test _has_novel_nonsynonymous ... ok Test has_var_groups ... ok test known_noncoding_het_snps ... ok Test _line2dict ... ok Test non_synon_variants ... ok Test _pc_id_and_read_depth_of_longest ... ok Test _to_cluster_summary_has_known_nonsynonymous ... ok Test _to_cluster_summary_has_nonsynonymous ... ok Test _to_cluster_summary_has_novel_nonsynonymous ... ok Test _to_cluster_summary_assembled ... ok test _filter_depths ... ok test _get_is_het_and_percent ... ok Test _has_nonsynonymous ... ok test __init__ ... ok Test _column_summary_data ... ok Test _load_file ... ok test _var_groups ... ok Test _variant_column_names_tuples_and_het_snps ... ok Test _add_phandango_colour_columns ... ok test_determine_cluster_cols (ariba.tests.summary_test.TestSummary) ... ok Test _distance_score_between_lists ... ok Test _distance_score_bewteen_values ... ok Test _filter_matrix_columns ... ok Test _filter_matrix_rows ... ok test gather_unfiltered_output_data ... ok Test init ... ok Test _load_fofn ... ok Test _load_input_files ... ok Test _matrix_to_csv ... ok Test _matrix_to_csv with remove_nas ... ok Test _newick_from_dist_matrix ... ok Test _to_matrix all columns ... ok Test _to_matrix with assembled column only ... ok Test _to_matrix with cluster columns only ... ok Test _to_matrix with groups ... ok Test _to_matrix with vars ... ok Test whole run to check csv ok (skip making tree) ... ok Test _write_distance_matrix ... ok test genbank_to_gene_coords ... ok test load_mutations ... ok test make_prepareref_dir ... ok test make_prepareref_files ... ok test report_to_resistance_dict ... ok test write_prepareref_fasta_file ... ok test write_prepareref_metadata_file ... ok test _cluster2seqs ... ok test _load_clusters ... ok test query with unknown query ... ok test _seq2cluster ... ok test _seqinfo ... ok Test get_all_versions ... WARNING: spades not found in path. Looked for spades.py ok test _fa_header_to_name_and_metadata ... ok test _fa_header_to_name_pieces ... ok test run ... ok ---------------------------------------------------------------------- Ran 356 tests in 239.438s OK (SKIP=2) create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:232: /usr/bin/python3 setup.py install --root /build/ariba-2.14.6+ds/debian/ariba running install running build running build_py running build_ext running build_scripts running install_lib creating /build/ariba-2.14.6+ds/debian/ariba/usr creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/vcfcall_ariba.cpython-39-aarch64-linux-gnu.so -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/fermilite_ariba.cpython-39-aarch64-linux-gnu.so -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/minimap_ariba.cpython-39-aarch64-linux-gnu.so -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/summary.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/report_flag_expander.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/vfdb_parser.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/ref_genes_getter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/refdata_query.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/read_filter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/versions.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/pubmlst_getter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/mic_plotter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/megares_zip_parser.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/megares_data_finder.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/faidx.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/ref_preparer.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/tb.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/sequence_metadata.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/reference_data.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/report_filter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/read_store.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/summary_cluster_variant.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/summary_cluster.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/summary_sample.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/mlst_profile.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/mlst_reporter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/histogram.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/clusters.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/samtools_variants.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/report.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/flag.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/cluster.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/cdhit.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/card_record.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/assembly_variants.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/assembly_compare.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/ref_seq_chooser.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/external_progs.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/link.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/scaffold_graph.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/bam_parse.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/mapping.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/common.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/assembly.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/sequence_variant.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/aln_to_metadata.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__pycache__/__init__.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__pycache__ creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20190102.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20181221.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20181115.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/NC_000962.3.gb -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20190102.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20181221.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/panel.20181115.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb_data/NC_000962.3.fa.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb_data creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/test_run_data/ref_seqs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/test_run_data creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/vfdb_parser_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/versions_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/test_refdata_query.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/tb_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/summary_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/summary_sample_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/summary_cluster_variant_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/summary_cluster_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/sequence_variant_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/sequence_metadata_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/scaffold_graph_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/samtools_variants_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/report_flag_expander_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/report_filter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/reference_data_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/ref_seq_chooser_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/ref_preparer_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/ref_genes_getter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/read_store_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/read_filter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/pubmlst_ref_preparer_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/pubmlst_getter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/ncbi_getter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/mlst_reporter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/mlst_profile_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/mic_plotter_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/megares_zip_parser_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/megares_data_finder_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/mapping_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/link_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/histogram_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/flag_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/faidx_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/external_progs_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/common_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/clusters_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/cluster_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/cdhit_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/card_record_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/bam_parse_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/assembly_variants_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/assembly_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/assembly_compare_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/aln_to_metadata_test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__pycache__/__init__.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__pycache__ creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/megares_zip_parser_write_files creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/clusters_run_with_tb.ref creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/ref_preparer_test_run.out creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/00.rename_info -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/00.info.txt -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data/refdata_query_prepareref copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_init_bad.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_not_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/vfdb_parser_test_run.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_profile_test.profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_to_matrix.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/tb_report_to_resistance_dict.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/dummy.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_clean.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_load_input_files.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_var_groups.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_too_long.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_run.expected.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_too_short.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_run.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_dummy_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_rename_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_remove_bad_genes.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_out.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_out.rename -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_profile_test.init.profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_flag_expander.run.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_ok.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_dummy_db.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/tb_genbank_to_gene_coords.gb -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_refdata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.make_link_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_load_fofn -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_fake_run.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_whole_run.out.csv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_fails.empty.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_to_matrix.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_data_info_file -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_getter.dbases.xml -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_compress_and_index_file.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_sequence.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_rename_sequences.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/test_common_cat_files.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_count_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_sequence_type.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_write_distance_matrix.distances -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.no_link_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_sequence.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_whole_run.in.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_load_input_files.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_sort_file.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_load_file.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.no_link_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.make_link_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_out.removed.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_load_summary_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_ok.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.3.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_fails.empty.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_load_annotations.csv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_dummy_db.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_ok.params.json -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_dummy_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_sort_file.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_load_mic_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_fix_in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_init_refdata.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_load_report_good.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refdata_query_prepareref.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_rename_sequences.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_cat_genes_match_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_fails.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/test_common_cat_files.in.3 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_sequence_type.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/test_common_cat_files.in.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/link_test_init.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/test_common_cat_files.in.1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.in.read_store -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_rename_seqs.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_init_good.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.profile.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_flag_expander.run.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_load_report_bad.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_write_all_links_to_file.out -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_fasta_file.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_run.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_init.fofn -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/report_filter_test_write_report.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_init_ok.rename.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/read_filter_test_run.in.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_test_whole_run.in.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/bam_parse_test_parse.bam -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_filter_bad_data.in.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/refcheck_test_check_ok.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cluster_test_count_reads_2.fq -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/data copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/vfdb_parser_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/reference_data_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/read_store_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/report_flag_expander_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/mic_plotter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/summary_sample_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/report_filter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/mlst_reporter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/read_filter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/aln_to_metadata_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/assembly_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/sequence_variant_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/sequence_metadata_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/pubmlst_getter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/summary_cluster_variant_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/tb_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/flag_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/link_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/faidx_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/histogram_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/ref_genes_getter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/external_progs_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/bam_parse_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/ref_preparer_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/samtools_variants_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/clusters_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/summary_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/mlst_profile_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/summary_cluster_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/test_refdata_query.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/assembly_compare_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/card_record_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/versions_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/megares_zip_parser_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/ref_seq_chooser_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/cdhit_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/cluster_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/megares_data_finder_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/scaffold_graph_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/__init__.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/common_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/mapping_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/ncbi_getter_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tests/assembly_variants_test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks creating /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/version.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/test.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/summary.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/run.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/reportfilter.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/refquery.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/pubmlstget.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/prepareref_tb.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/prepareref.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/micplot.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/getref.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/flag.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/expandflag.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/aln2meta.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__pycache__/__init__.cpython-39.pyc -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__pycache__ copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/expandflag.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/version.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/prepareref.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/run.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/summary.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/flag.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/micplot.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/prepareref_tb.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/reportfilter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/refquery.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/test.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/pubmlstget.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/pubmlstspecies.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/__init__.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/getref.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tasks/aln2meta.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/ref_seq_chooser.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/refdata_query.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/card_record.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/summary_cluster.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/vfdb_parser.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/report_flag_expander.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/scaffold_graph.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/assembly_compare.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/mlst_profile.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/pubmlst_ref_preparer.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/read_filter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/bam_parse.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/megares_data_finder.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/summary.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/megares_zip_parser.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/mlst_reporter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/samtools_variants.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/summary_cluster_variant.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/link.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/external_progs.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/flag.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/report_filter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/tb.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/read_store.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/pubmlst_getter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/sequence_variant.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/report.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/histogram.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/summary_sample.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/mic_plotter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/faidx.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/common.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/cdhit.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/ref_genes_getter.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/mapping.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/aln_to_metadata.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/cluster.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/ref_preparer.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/clusters.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/versions.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/sequence_metadata.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/__init__.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/reference_data.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/assembly_variants.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba copying /build/ariba-2.14.6+ds/.pybuild/cpython3_3.9_ariba/build/ariba/assembly.py -> /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py to pubmlst_ref_preparer_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/vfdb_parser_test.py to vfdb_parser_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/reference_data_test.py to reference_data_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/read_store_test.py to read_store_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/report_flag_expander_test.py to report_flag_expander_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/mic_plotter_test.py to mic_plotter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/summary_sample_test.py to summary_sample_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/report_filter_test.py to report_filter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/mlst_reporter_test.py to mlst_reporter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/read_filter_test.py to read_filter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/aln_to_metadata_test.py to aln_to_metadata_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/assembly_test.py to assembly_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/sequence_variant_test.py to sequence_variant_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/sequence_metadata_test.py to sequence_metadata_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/pubmlst_getter_test.py to pubmlst_getter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/summary_cluster_variant_test.py to summary_cluster_variant_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/tb_test.py to tb_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/flag_test.py to flag_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/link_test.py to link_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/faidx_test.py to faidx_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/histogram_test.py to histogram_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/ref_genes_getter_test.py to ref_genes_getter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/external_progs_test.py to external_progs_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/bam_parse_test.py to bam_parse_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/ref_preparer_test.py to ref_preparer_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/samtools_variants_test.py to samtools_variants_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/clusters_test.py to clusters_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/summary_test.py to summary_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/mlst_profile_test.py to mlst_profile_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/summary_cluster_test.py to summary_cluster_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/test_refdata_query.py to test_refdata_query.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/assembly_compare_test.py to assembly_compare_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/card_record_test.py to card_record_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/versions_test.py to versions_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/megares_zip_parser_test.py to megares_zip_parser_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/ref_seq_chooser_test.py to ref_seq_chooser_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/cdhit_test.py to cdhit_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/cluster_test.py to cluster_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/megares_data_finder_test.py to megares_data_finder_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/scaffold_graph_test.py to scaffold_graph_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/__init__.py to __init__.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/common_test.py to common_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/mapping_test.py to mapping_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/ncbi_getter_test.py to ncbi_getter_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tests/assembly_variants_test.py to assembly_variants_test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/version.py to version.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/prepareref.py to prepareref.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/run.py to run.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/summary.py to summary.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/flag.py to flag.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/micplot.py to micplot.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/prepareref_tb.py to prepareref_tb.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/refquery.py to refquery.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/test.py to test.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/pubmlstspecies.py to pubmlstspecies.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/__init__.py to __init__.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/getref.py to getref.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/refdata_query.py to refdata_query.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/card_record.py to card_record.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/mlst_profile.py to mlst_profile.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/read_filter.py to read_filter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/bam_parse.py to bam_parse.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/summary.py to summary.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/samtools_variants.py to samtools_variants.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/link.py to link.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/external_progs.py to external_progs.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/flag.py to flag.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/report_filter.py to report_filter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/tb.py to tb.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/read_store.py to read_store.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/pubmlst_getter.py to pubmlst_getter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/report.py to report.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/histogram.py to histogram.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/summary_sample.py to summary_sample.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/faidx.py to faidx.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/common.py to common.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/cdhit.py to cdhit.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/mapping.py to mapping.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/cluster.py to cluster.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/clusters.py to clusters.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/versions.py to versions.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/__init__.py to __init__.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/reference_data.py to reference_data.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-39.pyc byte-compiling /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba/assembly.py to assembly.cpython-39.pyc running install_egg_info running egg_info creating ariba.egg-info writing ariba.egg-info/PKG-INFO writing dependency_links to ariba.egg-info/dependency_links.txt writing requirements to ariba.egg-info/requires.txt writing top-level names to ariba.egg-info/top_level.txt writing manifest file 'ariba.egg-info/SOURCES.txt' reading manifest file 'ariba.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching '*.h' under directory 'third_party' writing manifest file 'ariba.egg-info/SOURCES.txt' Copying ariba.egg-info to /build/ariba-2.14.6+ds/debian/ariba/usr/lib/python3.9/dist-packages/ariba-2.14.6.egg-info Skipping SOURCES.txt running install_scripts creating /build/ariba-2.14.6+ds/debian/ariba/usr/bin copying build/scripts-3.9/ariba -> /build/ariba-2.14.6+ds/debian/ariba/usr/bin changing mode of /build/ariba-2.14.6+ds/debian/ariba/usr/bin/ariba to 755 dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/build/ariba-2.14.6+ds' mkdir -p /build/ariba-2.14.6+ds/debian/man asciidoctor -a docdate='' -b manpage -o /build/ariba-2.14.6+ds/debian/man/ariba.1 /build/ariba-2.14.6+ds/debian/ariba.1.adoc dh_installman -- make[1]: Leaving directory '/build/ariba-2.14.6+ds' dh_python3 -O--buildsystem=pybuild dh_installsystemduser -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ariba/usr/lib/python3/dist-packages/vcfcall_ariba.cpython-39-aarch64-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: package ariba: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: package ariba: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'ariba-dbgsym' in '../ariba-dbgsym_2.14.6+ds-1_arm64.deb'. dpkg-deb: building package 'ariba' in '../ariba_2.14.6+ds-1_arm64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../ariba_2.14.6+ds-1_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) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: user script /srv/workspace/pbuilder/25398/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/25398/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/25398 and its subdirectories I: Current time: Wed Jul 7 11:13:22 +14 2021 I: pbuilder-time-stamp: 1625606002