https://launchpad.net/ubuntu/+source/ariba/2.14.4+ds-2.1/+build/19212893 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux lcy01-amd64-014 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:44 UTC 2020 x86_64 Buildd toolchain package versions: launchpad-buildd_189 python-lpbuildd_189 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.9 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 21 May 15:53:47 ntpdate[1914]: adjust time server 10.211.37.1 offset 0.026416 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19212893 --image-type chroot /home/buildd/filecache-default/7f6882774d93a6ce12d34cd2f4e4b83a707bcc6e Creating target for build PACKAGEBUILD-19212893 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19212893 Starting target for build PACKAGEBUILD-19212893 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19212893 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19212893 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19212893 Updating target for build PACKAGEBUILD-19212893 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [268 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [119 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main amd64 Packages [971 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [507 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe amd64 Packages [8715 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5172 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 Packages [62.0 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [31.7 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 Packages [515 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [262 kB] Fetched 16.8 MB in 8s (2099 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-common binutils-x86-64-linux-gnu bsdutils cpp-9 dash debconf e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv libacl1 libapparmor1 libapt-pkg6.0 libasan5 libatomic1 libbinutils libblkid1 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgomp1 libidn2-0 libitm1 libkmod2 liblsan0 libmount1 libncurses6 libncursesw6 libperl5.30 libprocps8 libquadmath0 libseccomp2 libsmartcols1 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 linux-libc-dev logsave make mount ncurses-base ncurses-bin perl perl-base perl-modules-5.30 procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata util-linux 77 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 54.7 MB of archives. After this operation, 417 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main amd64 libcrypt-dev amd64 1:4.4.15-1ubuntu1 [104 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main amd64 libcrypt1 amd64 1:4.4.15-1ubuntu1 [78.2 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main amd64 base-files amd64 11ubuntu7 [60.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 bsdutils amd64 1:2.35.1-5ubuntu2 [86.8 kB] Get:5 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 perl-modules-5.30 all 5.30.2-1 [2740 kB] Get:6 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libperl5.30 amd64 5.30.2-1 [3952 kB] Get:7 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 perl amd64 5.30.2-1 [224 kB] Get:8 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 perl-base amd64 5.30.2-1 [1513 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main amd64 debconf all 1.5.74 [121 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main amd64 dash amd64 0.5.10.2-7 [86.3 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main amd64 ncurses-bin amd64 6.2-1 [172 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libblkid1 amd64 2.35.1-5ubuntu2 [133 kB] Get:13 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libuuid1 amd64 2.35.1-5ubuntu2 [22.2 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libfdisk1 amd64 2.35.1-5ubuntu2 [171 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libmount1 amd64 2.35.1-5ubuntu2 [145 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main amd64 libncurses6 amd64 6.2-1 [101 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main amd64 libncursesw6 amd64 6.2-1 [132 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main amd64 libtinfo6 amd64 6.2-1 [87.1 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libsmartcols1 amd64 2.35.1-5ubuntu2 [95.7 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 fdisk amd64 2.35.1-5ubuntu2 [123 kB] Get:21 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 util-linux amd64 2.35.1-5ubuntu2 [1050 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main amd64 ncurses-base all 6.2-1 [18.7 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main amd64 sysvinit-utils amd64 2.96-3ubuntu1 [20.6 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main amd64 libatomic1 amd64 10.1.0-2ubuntu1 [9284 B] Get:25 http://ftpmaster.internal/ubuntu groovy/main amd64 libubsan1 amd64 10.1.0-2ubuntu1 [136 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main amd64 libtsan0 amd64 10.1.0-2ubuntu1 [320 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main amd64 libquadmath0 amd64 10.1.0-2ubuntu1 [146 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main amd64 liblsan0 amd64 10.1.0-2ubuntu1 [144 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main amd64 libitm1 amd64 10.1.0-2ubuntu1 [26.4 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main amd64 libgomp1 amd64 10.1.0-2ubuntu1 [101 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main amd64 gcc-10-base amd64 10.1.0-2ubuntu1 [20.2 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main amd64 libgcc-s1 amd64 10.1.0-2ubuntu1 [41.6 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main amd64 libcc1-0 amd64 10.1.0-2ubuntu1 [41.1 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main amd64 libstdc++6 amd64 10.1.0-2ubuntu1 [502 kB] Get:35 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 systemd-sysv amd64 245.5-3ubuntu1 [10.3 kB] Get:36 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 systemd-timesyncd amd64 245.5-3ubuntu1 [27.9 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main amd64 libacl1 amd64 2.2.53-8 [18.9 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main amd64 libapparmor1 amd64 2.13.3-7ubuntu6 [34.3 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main amd64 libcap2 amd64 1:2.34-2 [17.9 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main amd64 libcryptsetup12 amd64 2:2.3.1-1ubuntu1 [192 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main amd64 libidn2-0 amd64 2.3.0-1 [52.6 kB] Get:42 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libkmod2 amd64 27+20200310-2ubuntu1 [44.1 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main amd64 libseccomp2 amd64 2.4.3-1ubuntu2 [42.0 kB] Get:44 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 mount amd64 2.35.1-5ubuntu2 [118 kB] Get:45 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 systemd amd64 245.5-3ubuntu1 [3798 kB] Get:46 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libsystemd0 amd64 245.5-3ubuntu1 [267 kB] Get:47 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libudev1 amd64 245.5-3ubuntu1 [74.6 kB] Get:48 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libapt-pkg6.0 amd64 2.1.4 [841 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main amd64 gpgv amd64 2.2.20-1ubuntu1 [200 kB] Get:50 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 apt amd64 2.1.4 [1289 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main amd64 logsave amd64 1.45.6-1ubuntu1 [10.3 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main amd64 libext2fs2 amd64 1.45.6-1ubuntu1 [184 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main amd64 e2fsprogs amd64 1.45.6-1ubuntu1 [529 kB] Get:54 http://ftpmaster.internal/ubuntu groovy/main amd64 libcom-err2 amd64 1.45.6-1ubuntu1 [9664 B] Get:55 http://ftpmaster.internal/ubuntu groovy/main amd64 libprocps8 amd64 2:3.3.16-4ubuntu1 [32.9 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main amd64 libss2 amd64 1.45.6-1ubuntu1 [11.3 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main amd64 procps amd64 2:3.3.16-4ubuntu1 [232 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main amd64 libsqlite3-0 amd64 3.31.1-5 [548 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main amd64 tzdata all 2020a-0ubuntu1 [293 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main amd64 libctf0 amd64 2.34-7ubuntu1 [46.6 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main amd64 binutils-x86-64-linux-gnu amd64 2.34-7ubuntu1 [1613 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main amd64 libbinutils amd64 2.34-7ubuntu1 [474 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main amd64 binutils amd64 2.34-7ubuntu1 [3376 B] Get:64 http://ftpmaster.internal/ubuntu groovy/main amd64 binutils-common amd64 2.34-7ubuntu1 [207 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main amd64 libctf-nobfd0 amd64 2.34-7ubuntu1 [47.2 kB] Get:66 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libasan5 amd64 9.3.0-13ubuntu1 [395 kB] Get:67 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 g++-9 amd64 9.3.0-13ubuntu1 [8403 kB] Get:68 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 gcc-9 amd64 9.3.0-13ubuntu1 [8239 kB] Get:69 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libstdc++-9-dev amd64 9.3.0-13ubuntu1 [1714 kB] Get:70 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libgcc-9-dev amd64 9.3.0-13ubuntu1 [2360 kB] Get:71 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 cpp-9 amd64 9.3.0-13ubuntu1 [7490 kB] Get:72 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 gcc-9-base amd64 9.3.0-13ubuntu1 [19.6 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main amd64 gpg amd64 2.2.20-1ubuntu1 [485 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main amd64 gpgconf amd64 2.2.20-1ubuntu1 [124 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main amd64 gpg-agent amd64 2.2.20-1ubuntu1 [232 kB] Get:76 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 linux-libc-dev amd64 5.4.0-29.33 [1098 kB] Get:77 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 make amd64 4.3-1 [168 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 54.7 MB in 2s (22.5 MB/s) (Reading database ... 12816 files and directories currently installed.) 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Setting up cpp-9 (9.3.0-13ubuntu1) ... Setting up binutils-x86-64-linux-gnu (2.34-7ubuntu1) ... Setting up binutils (2.34-7ubuntu1) ... Setting up libgcc-9-dev:amd64 (9.3.0-13ubuntu1) ... Setting up gcc-9 (9.3.0-13ubuntu1) ... Setting up libstdc++-9-dev:amd64 (9.3.0-13ubuntu1) ... Setting up g++-9 (9.3.0-13ubuntu1) ... Setting up systemd-timesyncd (245.5-3ubuntu1) ... Setting up systemd (245.5-3ubuntu1) ... Initializing machine ID from KVM UUID. Setting up systemd-sysv (245.5-3ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19212893 amd64 groovy-proposed -c chroot:build-PACKAGEBUILD-19212893 --arch=amd64 --dist=groovy-proposed --nolog -A ariba_2.14.4+ds-2.1.dsc Initiating build PACKAGEBUILD-19212893 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-179-generic #209-Ubuntu SMP Fri Apr 24 17:48:44 UTC 2020 x86_64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on lcy01-amd64-014.buildd +==============================================================================+ | ariba 2.14.4+ds-2.1 (amd64) 21 May 2020 15:54 | +==============================================================================+ Package: ariba Version: 2.14.4+ds-2.1 Source Version: 2.14.4+ds-2.1 Distribution: groovy-proposed Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 I: NOTICE: Log filtering will replace 'build/ariba-0IJCOa/ariba-2.14.4+ds' with '<>' I: NOTICE: Log filtering will replace 'build/ariba-0IJCOa' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19212893/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- ariba_2.14.4+ds-2.1.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-R3wUbO/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-R3wUbO/apt_archive ./ InRelease Get:2 copy:/<>/resolver-R3wUbO/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-R3wUbO/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-R3wUbO/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-R3wUbO/apt_archive ./ Packages [524 B] Fetched 2857 B in 0s (136 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install core build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-R3wUbO/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (0 B/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12824 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... Merged Build-Depends: debhelper-compat (= 12), 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 Filtered Build-Depends: debhelper-compat (= 12), 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 'sbuild-build-depends-ariba-dummy' in '/<>/resolver-r5dBHn/apt_archive/sbuild-build-depends-ariba-dummy.deb'. Ign:1 copy:/<>/resolver-r5dBHn/apt_archive ./ InRelease Get:2 copy:/<>/resolver-r5dBHn/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-r5dBHn/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-r5dBHn/apt_archive ./ Sources [365 B] Get:5 copy:/<>/resolver-r5dBHn/apt_archive ./ Packages [690 B] Fetched 3174 B in 0s (203 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install ariba build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev blt bowtie2 bsdmainutils cd-hit debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-lyx gawk gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbrotli1 libbsd0 libcapnp-0.7.0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgsl25 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libicu66 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libminimap-dev libminimap0 libmpdec2 libmurmurhash2 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtbb2 libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libyaml-0-2 m4 man-db mash mime-support mummer node-jquery po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-biopython python3-bs4 python3-cycler python3-dateutil python3-dendropy python3-dev python3-distutils python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-nose python3-numpy python3-pil python3-pkg-resources python3-pymummer python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-setuptools python3-six python3-soupsieve python3-tk python3.8 python3.8-dev python3.8-minimal rake ruby ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration samtools tk8.6-blt2.5 ttf-bitstream-vera ucf x11-common zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo bowtie2-examples wamerican | wordlist whois vacation dh-make gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-rdflib python3-renderpm python3-psycopg2 python3-scipy raxml t-coffee wise w3-dtd-mathml python-cycler-doc dvipng ffmpeg gir1.2-gtk-3.0 ghostscript inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft python-nose-doc gfortran python-numpy-doc python3-pytest python3-numpy-dbg python-pil-doc python3-pil-dbg python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-setuptools-doc tix python3-tk-dbg python3.8-venv python3.8-doc binfmt-support ri ruby-dev bundler Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+ python3-chardet python3-lxml python3-olefile python3-renderpm zip fonts-lato cwltool The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev blt bowtie2 bsdmainutils cd-hit debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-lyx gawk gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasn1-8-heimdal libblas3 libbrotli1 libbsd0 libcapnp-0.7.0 libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgsl25 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libicu66 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblocale-gettext-perl libmagic-mgc libmagic1 libminimap-dev libminimap0 libmpdec2 libmurmurhash2 libnghttp2-14 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libruby2.7 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtbb2 libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp6 libwebpdemux2 libwebpmux3 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libyaml-0-2 m4 man-db mash mime-support mummer node-jquery po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-biopython python3-bs4 python3-cycler python3-dateutil python3-dendropy python3-dev python3-distutils python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-nose python3-numpy python3-pil python3-pkg-resources python3-pymummer python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-setuptools python3-six python3-soupsieve python3-tk python3.8 python3.8-dev python3.8-minimal rake ruby ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration samtools sbuild-build-depends-ariba-dummy tk8.6-blt2.5 ttf-bitstream-vera ucf x11-common zlib1g-dev 0 upgraded, 170 newly installed, 0 to remove and 0 not upgraded. Need to get 66.9 MB of archives. After this operation, 267 MB of additional disk space will be used. Get:1 copy:/<>/resolver-r5dBHn/apt_archive ./ sbuild-build-depends-ariba-dummy 0.invalid.0 [1020 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main amd64 liblocale-gettext-perl amd64 1.07-4 [17.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main amd64 libpython3.8-minimal amd64 3.8.3-1 [714 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main amd64 libexpat1 amd64 2.2.9-1build1 [73.3 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main amd64 python3.8-minimal amd64 3.8.3-1 [1897 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-minimal amd64 3.8.2-0ubuntu2 [23.6 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main amd64 mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main amd64 libmpdec2 amd64 2.4.2-3 [81.1 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main amd64 libpython3.8-stdlib amd64 3.8.3-1 [1668 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main amd64 python3.8 amd64 3.8.3-1 [369 kB] Get:11 http://ftpmaster.internal/ubuntu groovy/main amd64 libpython3-stdlib amd64 3.8.2-0ubuntu2 [7068 B] Get:12 http://ftpmaster.internal/ubuntu groovy/main amd64 python3 amd64 3.8.2-0ubuntu2 [47.6 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main amd64 libbsd0 amd64 0.10.0-1 [45.4 kB] Get:14 http://ftpmaster.internal/ubuntu groovy/main amd64 bsdmainutils amd64 11.1.2ubuntu3 [181 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main amd64 libuchardet0 amd64 0.0.6-3build1 [65.2 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main amd64 groff-base amd64 1.22.4-5 [847 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main amd64 libpipeline1 amd64 1.5.2-2build1 [27.7 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main amd64 man-db amd64 2.9.1-1 [1112 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main amd64 libsigsegv2 amd64 2.12-2 [13.9 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main amd64 gawk amd64 1:5.0.1+dfsg-1 [418 kB] Get:21 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libmagic-mgc amd64 1:5.38-5 [218 kB] Get:22 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libmagic1 amd64 1:5.38-5 [76.0 kB] Get:23 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 file amd64 1:5.38-5 [23.3 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main amd64 libelf1 amd64 0.176-1.1build1 [44.0 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main amd64 libglib2.0-0 amd64 2.64.2-1 [1287 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main amd64 libicu66 amd64 66.1-2ubuntu2 [8520 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main amd64 libxml2 amd64 2.9.10+dfsg-5 [640 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main amd64 libyaml-0-2 amd64 0.2.2-1 [48.9 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-pkg-resources all 46.1.3-1 [127 kB] Get:30 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 ucf all 3.0041 [56.0 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main amd64 gettext-base amd64 0.19.8.1-10build1 [50.2 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main amd64 libkrb5support0 amd64 1.17-6ubuntu4 [30.9 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main amd64 libk5crypto3 amd64 1.17-6ubuntu4 [80.2 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main amd64 libkeyutils1 amd64 1.6.1-2ubuntu1 [10.1 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main amd64 libkrb5-3 amd64 1.17-6ubuntu4 [330 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main amd64 libgssapi-krb5-2 amd64 1.17-6ubuntu4 [121 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main amd64 libpsl5 amd64 0.21.0-1ubuntu1 [51.5 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main amd64 libxau6 amd64 1:1.0.9-0ubuntu1 [7488 B] Get:39 http://ftpmaster.internal/ubuntu groovy/main amd64 libxdmcp6 amd64 1:1.1.3-0ubuntu1 [10.6 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main amd64 libxcb1 amd64 1.14-2 [44.7 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main amd64 libx11-data all 2:1.6.9-2ubuntu1 [113 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main amd64 libx11-6 amd64 2:1.6.9-2ubuntu1 [573 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main amd64 libxext6 amd64 2:1.3.4-0ubuntu1 [29.1 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main amd64 rubygems-integration all 1.16 [5092 B] Get:45 http://ftpmaster.internal/ubuntu groovy/main amd64 rake all 13.0.1-4 [61.6 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main amd64 ruby-minitest all 5.13.0-1 [40.9 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main amd64 ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main amd64 ruby-power-assert all 1.1.7-1 [11.4 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main amd64 ruby-test-unit all 3.3.5-1 [73.2 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main amd64 ruby-xmlrpc all 0.3.0-2 [23.8 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main amd64 libruby2.7 amd64 2.7.1-3 [3529 kB] Get:52 http://ftpmaster.internal/ubuntu groovy/main amd64 ruby2.7 amd64 2.7.1-3 [95.6 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main amd64 ruby amd64 1:2.7+1 [5412 B] Get:54 http://ftpmaster.internal/ubuntu groovy/universe amd64 ruby-asciidoctor all 2.0.10-2 [166 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/universe amd64 asciidoctor all 2.0.10-2 [40.3 kB] Get:56 http://ftpmaster.internal/ubuntu groovy/main amd64 m4 amd64 1.4.18-4 [199 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main amd64 autoconf all 2.69-11.1 [321 kB] Get:58 http://ftpmaster.internal/ubuntu groovy/main amd64 autotools-dev all 20180224.1 [39.6 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main amd64 automake all 1:1.16.1-4ubuntu6 [522 kB] Get:60 http://ftpmaster.internal/ubuntu groovy/main amd64 autopoint all 0.19.8.1-10build1 [412 kB] Get:61 http://ftpmaster.internal/ubuntu groovy/main amd64 libtcl8.6 amd64 8.6.10+dfsg-1 [902 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main amd64 libfreetype6 amd64 2.10.1-2 [341 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/universe amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main amd64 fontconfig-config all 2.13.1-2ubuntu3 [28.8 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main amd64 libfontconfig1 amd64 2.13.1-2ubuntu3 [114 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main amd64 libxrender1 amd64 1:0.9.10-1 [18.7 kB] Get:67 http://ftpmaster.internal/ubuntu groovy/main amd64 libxft2 amd64 2.3.3-0ubuntu1 [39.2 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main amd64 x11-common all 1:7.7+19ubuntu14 [22.3 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main amd64 libxss1 amd64 1:1.2.3-1 [8140 B] Get:70 http://ftpmaster.internal/ubuntu groovy/main amd64 libtk8.6 amd64 8.6.10-1 [714 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4 [572 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main amd64 blt amd64 2.5.3+dfsg-4 [4944 B] Get:73 http://ftpmaster.internal/ubuntu groovy/universe amd64 cd-hit amd64 4.8.1-2build1 [524 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main amd64 libtool all 2.4.6-14 [161 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main amd64 dh-autoreconf all 19 [16.1 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main amd64 libdebhelper-perl all 13ubuntu1 [62.5 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main amd64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main amd64 libsub-override-perl all 0.09-2 [9532 B] Get:79 http://ftpmaster.internal/ubuntu groovy/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [16.2 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main amd64 dh-strip-nondeterminism all 1.8.0-1 [5228 B] Get:81 http://ftpmaster.internal/ubuntu groovy/main amd64 dwz amd64 0.13-5 [151 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main amd64 libcroco3 amd64 0.6.13-1 [82.5 kB] Get:83 http://ftpmaster.internal/ubuntu groovy/main amd64 gettext amd64 0.19.8.1-10build1 [895 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main amd64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:85 http://ftpmaster.internal/ubuntu groovy/main amd64 po-debconf all 1.0.21 [233 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main amd64 debhelper all 13ubuntu1 [877 kB] Get:87 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 python3-lib2to3 all 3.8.3-2 [74.1 kB] Get:88 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 python3-distutils all 3.8.3-2 [140 kB] Get:89 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 dh-python all 4.20200315 [85.8 kB] Get:90 http://ftpmaster.internal/ubuntu groovy/main amd64 libbrotli1 amd64 1.0.7-6.1 [265 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main amd64 libroken18-heimdal amd64 7.7.0+dfsg-2 [41.8 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/main amd64 libasn1-8-heimdal amd64 7.7.0+dfsg-2 [181 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/main amd64 libheimbase1-heimdal amd64 7.7.0+dfsg-2 [29.7 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/main amd64 libhcrypto4-heimdal amd64 7.7.0+dfsg-2 [88.0 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/main amd64 libwind0-heimdal amd64 7.7.0+dfsg-2 [47.6 kB] Get:96 http://ftpmaster.internal/ubuntu groovy/main amd64 libhx509-5-heimdal amd64 7.7.0+dfsg-2 [107 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main amd64 libkrb5-26-heimdal amd64 7.7.0+dfsg-2 [207 kB] Get:98 http://ftpmaster.internal/ubuntu groovy/main amd64 libheimntlm0-heimdal amd64 7.7.0+dfsg-2 [15.1 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main amd64 libgssapi3-heimdal amd64 7.7.0+dfsg-2 [96.5 kB] Get:100 http://ftpmaster.internal/ubuntu groovy/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2 [14.9 kB] Get:101 http://ftpmaster.internal/ubuntu groovy/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2 [49.3 kB] Get:102 http://ftpmaster.internal/ubuntu groovy/main amd64 libldap-common all 2.4.49+dfsg-2ubuntu2 [17.4 kB] Get:103 http://ftpmaster.internal/ubuntu groovy/main amd64 libldap-2.4-2 amd64 2.4.49+dfsg-2ubuntu2 [156 kB] Get:104 http://ftpmaster.internal/ubuntu groovy/main amd64 libnghttp2-14 amd64 1.40.0-1build1 [78.7 kB] Get:105 http://ftpmaster.internal/ubuntu groovy/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2build1 [54.9 kB] Get:106 http://ftpmaster.internal/ubuntu groovy/main amd64 libssh-4 amd64 0.9.4-1ubuntu1 [170 kB] Get:107 http://ftpmaster.internal/ubuntu groovy/main amd64 libcurl3-gnutls amd64 7.68.0-1ubuntu2 [231 kB] Get:108 http://ftpmaster.internal/ubuntu groovy/universe amd64 libdeflate0 amd64 1.6-1 [54.8 kB] Get:109 http://ftpmaster.internal/ubuntu groovy/universe amd64 libhts3 amd64 1.10.2-3 [349 kB] Get:110 http://ftpmaster.internal/ubuntu groovy/universe amd64 samtools amd64 1.10-3 [496 kB] Get:111 http://ftpmaster.internal/ubuntu groovy/universe amd64 fastaq all 3.17.0-3 [47.7 kB] Get:112 http://ftpmaster.internal/ubuntu groovy/universe amd64 fonts-lyx all 2.3.4.2-2 [154 kB] Get:113 http://ftpmaster.internal/ubuntu groovy/universe amd64 help2man amd64 1.47.15 [173 kB] Get:114 http://ftpmaster.internal/ubuntu groovy/main amd64 libblas3 amd64 3.9.0-2 [141 kB] Get:115 http://ftpmaster.internal/ubuntu groovy/main amd64 libcapnp-0.7.0 amd64 0.7.0-6 [1047 kB] Get:116 http://ftpmaster.internal/ubuntu groovy/main amd64 libexpat1-dev amd64 2.2.9-1build1 [116 kB] Get:117 http://ftpmaster.internal/ubuntu groovy/universe amd64 libfml0 amd64 0.1-13 [70.4 kB] Get:118 http://ftpmaster.internal/ubuntu groovy/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-2ubuntu1 [156 kB] Get:119 http://ftpmaster.internal/ubuntu groovy/universe amd64 libfml-dev amd64 0.1-13 [81.0 kB] Get:120 http://ftpmaster.internal/ubuntu groovy/main amd64 libgfortran5 amd64 10.1.0-2ubuntu1 [734 kB] Get:121 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 libgslcblas0 amd64 2.6+dfsg-2 [84.7 kB] Get:122 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 libgsl25 amd64 2.6+dfsg-2 [907 kB] Get:123 http://ftpmaster.internal/ubuntu groovy/main amd64 libimagequant0 amd64 2.12.2-1.1 [31.4 kB] Get:124 http://ftpmaster.internal/ubuntu groovy/main amd64 libjpeg-turbo8 amd64 2.0.3-0ubuntu1 [118 kB] Get:125 http://ftpmaster.internal/ubuntu groovy/main amd64 libjpeg8 amd64 8c-2ubuntu8 [2194 B] Get:126 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 node-jquery all 3.5.1+dfsg-3 [309 kB] Get:127 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 libjs-jquery all 3.5.1+dfsg-3 [2308 B] Get:128 http://ftpmaster.internal/ubuntu groovy/universe amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:129 http://ftpmaster.internal/ubuntu groovy/main amd64 liblapack3 amd64 3.9.0-2 [2156 kB] Get:130 http://ftpmaster.internal/ubuntu groovy/main amd64 liblcms2-2 amd64 2.9-4 [140 kB] Get:131 http://ftpmaster.internal/ubuntu groovy/universe amd64 libminimap0 amd64 0.2-5 [23.1 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python3-reportlab-accel amd64 3.5.34-1ubuntu1 [19.4 kB] Get:152 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-pil amd64 7.0.0-4build1 [361 kB] Get:153 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-reportlab all 3.5.34-1ubuntu1 [546 kB] Get:154 http://ftpmaster.internal/ubuntu groovy-proposed/universe amd64 python3-biopython amd64 1.76+dfsg-2 [1399 kB] Get:155 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-soupsieve all 2.0-1 [28.7 kB] Get:156 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-bs4 all 4.9.0-2 [85.1 kB] Get:157 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-six all 1.14.0-3 [12.1 kB] Get:158 http://ftpmaster.internal/ubuntu groovy/universe amd64 python3-cycler all 0.10.0-3 [8132 B] Get:159 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-dateutil all 2.8.1-4 [79.8 kB] Get:160 http://ftpmaster.internal/ubuntu groovy/universe amd64 python3-dendropy all 4.4.0-2 [266 kB] Get:161 http://ftpmaster.internal/ubuntu groovy/universe amd64 python3-kiwisolver amd64 1.0.1-3build1 [61.3 kB] Get:162 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-pyparsing all 2.4.7-1 [61.4 kB] Get:163 http://ftpmaster.internal/ubuntu groovy/universe amd64 python3-matplotlib amd64 3.1.2-1ubuntu4 [4459 kB] Get:164 http://ftpmaster.internal/ubuntu groovy/universe amd64 python3-nose all 1.3.7-5 [116 kB] Get:165 http://ftpmaster.internal/ubuntu groovy/universe amd64 python3-pymummer all 0.10.3-2 [9312 B] Get:166 http://ftpmaster.internal/ubuntu groovy/universe amd64 python3-pysam amd64 0.15.4+ds-3 [1865 kB] Get:167 http://ftpmaster.internal/ubuntu groovy/main amd64 python3-setuptools all 46.1.3-1 [325 kB] Get:168 http://ftpmaster.internal/ubuntu groovy-proposed/main amd64 python3-tk amd64 3.8.3-2 [96.4 kB] Get:169 http://ftpmaster.internal/ubuntu groovy/universe amd64 libtbb2 amd64 2020.2-2 [124 kB] Get:170 http://ftpmaster.internal/ubuntu groovy/universe amd64 bowtie2 amd64 2.4.1-4 [1326 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 66.9 MB in 3s (21.6 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12824 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... Selecting previously unselected package libpython3.8-minimal:amd64. Preparing to unpack .../libpython3.8-minimal_3.8.3-1_amd64.deb ... Unpacking libpython3.8-minimal:amd64 (3.8.3-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.2.9-1build1_amd64.deb ... Unpacking libexpat1:amd64 (2.2.9-1build1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.3-1_amd64.deb ... Unpacking python3.8-minimal (3.8.3-1) ... Setting up libpython3.8-minimal:amd64 (3.8.3-1) ... Setting up libexpat1:amd64 (2.2.9-1build1) ... Setting up python3.8-minimal (3.8.3-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13129 files and directories currently installed.) 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Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:amd64 (1.17-6ubuntu4) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up libminimap-dev (0.2-5) ... Setting up libssh-4:amd64 (0.9.4-1ubuntu1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up libx11-6:amd64 (2:1.6.9-2ubuntu1) ... Setting up python3-dateutil (2.8.1-4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2build1) ... Setting up libfontconfig1:amd64 (2.13.1-2ubuntu3) ... Setting up libjs-jquery (3.5.1+dfsg-3) ... Setting up python3-lib2to3 (3.8.3-2) ... Setting up python3-soupsieve (2.0-1) ... Setting up python3-pkg-resources (46.1.3-1) ... Setting up python3-distutils (3.8.3-2) ... Setting up dh-python (4.20200315) ... Setting up gettext (0.19.8.1-10build1) ... Setting up python3-setuptools (46.1.3-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libhx509-5-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libxext6:amd64 (2:1.3.4-0ubuntu1) ... Setting up python3-all (3.8.2-0ubuntu2) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-nose (1.3.7-5) ... Setting up python3-bs4 (4.9.0-2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-pil:amd64 (7.0.0-4build1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up libpython3.8-dev:amd64 (3.8.3-1) ... Setting up python3-kiwisolver (1.0.1-3build1) ... Setting up python3-numpy (1:1.18.4-1) ... Setting up python3.8-dev (3.8.3-1) ... Setting up python3-reportlab (3.5.34-1ubuntu1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up python3-biopython (1.76+dfsg-2) ... Setting up python3-dendropy (4.4.0-2) ... Setting up libkrb5-26-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up python3-matplotlib (3.1.2-1ubuntu4) ... Setting up libxft2:amd64 (2.3.3-0ubuntu1) ... Setting up libpython3-dev:amd64 (3.8.2-0ubuntu2) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:amd64 (8.6.10-1) ... Setting up libheimntlm0-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:amd64 (7.7.0+dfsg-2) ... Setting up libpython3-all-dev:amd64 (3.8.2-0ubuntu2) ... Setting up python3-dev (3.8.2-0ubuntu2) ... Setting up python3-all-dev (3.8.2-0ubuntu2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4) ... Setting up blt (2.5.3+dfsg-4) ... Setting up libldap-2.4-2:amd64 (2.4.49+dfsg-2ubuntu2) ... Setting up python3-tk:amd64 (3.8.3-2) ... Setting up libcurl3-gnutls:amd64 (7.68.0-1ubuntu2) ... Setting up libhts3:amd64 (1.10.2-3) ... Setting up python3-pysam (0.15.4+ds-3) ... Setting up samtools (1.10-3) ... 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Processing triggers for systemd (245.5-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-179-generic amd64 (x86_64) Toolchain package versions: binutils_2.34-7ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-13ubuntu1 gcc-9_9.3.0-13ubuntu1 libc6-dev_2.31-0ubuntu9 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-2ubuntu1 linux-libc-dev_5.4.0-29.33 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.4 asciidoctor_2.0.10-2 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu6 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 binutils_2.34-7ubuntu1 binutils-common_2.34-7ubuntu1 binutils-x86-64-linux-gnu_2.34-7ubuntu1 blt_2.5.3+dfsg-4 bowtie2_2.4.1-4 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.35.1-5ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110ubuntu1 cd-hit_4.8.1-2build1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-13ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20200315 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 fastaq_3.17.0-3 fdisk_2.35.1-5ubuntu2 file_1:5.38-5 findutils_4.7.0-1ubuntu1 fontconfig-config_2.13.1-2ubuntu3 fonts-lyx_2.3.4.2-2 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-13ubuntu1 gawk_1:5.0.1+dfsg-1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-2ubuntu1 gcc-9_9.3.0-13ubuntu1 gcc-9-base_9.3.0-13ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-0ubuntu4 help2man_1.47.15 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.4 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2 libasan5_9.3.0-13ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-2 libassuan0_2.5.3-7ubuntu2 libatomic1_10.1.0-2ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu6 libaudit1_1:2.8.5-2ubuntu6 libbinutils_2.34-7ubuntu1 libblas3_3.9.0-2 libblkid1_2.35.1-5ubuntu2 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.31-0ubuntu9 libc-dev-bin_2.31-0ubuntu9 libc6_2.31-0ubuntu9 libc6-dev_2.31-0ubuntu9 libcap-ng0_0.7.9-2.1build1 libcap2_1:2.34-2 libcapnp-0.7.0_0.7.0-6 libcc1-0_10.1.0-2ubuntu1 libcom-err2_1.45.6-1ubuntu1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.15-1ubuntu1 libcrypt1_1:4.4.15-1ubuntu1 libcryptsetup12_2:2.3.1-1ubuntu1 libctf-nobfd0_2.34-7ubuntu1 libctf0_2.34-7ubuntu1 libcurl3-gnutls_7.68.0-1ubuntu2 libdb5.3_5.3.28+dfsg1-0.6ubuntu2 libdebconfclient0_0.251ubuntu1 libdebhelper-perl_13ubuntu1 libdeflate0_1.6-1 libdevmapper1.02.1_2:1.02.167-1ubuntu1 libdpkg-perl_1.19.7ubuntu3 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libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12build1 libperl5.30_5.30.2-1 libpipeline1_1.5.2-2build1 libpng16-16_1.6.37-2 libprocps8_2:3.3.16-4ubuntu1 libpsl5_0.21.0-1ubuntu1 libpython3-all-dev_3.8.2-0ubuntu2 libpython3-dev_3.8.2-0ubuntu2 libpython3-stdlib_3.8.2-0ubuntu2 libpython3.8_3.8.3-1 libpython3.8-dev_3.8.3-1 libpython3.8-minimal_3.8.3-1 libpython3.8-stdlib_3.8.3-1 libquadmath0_10.1.0-2ubuntu1 libreadline8_8.0-4 libroken18-heimdal_7.7.0+dfsg-2 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libruby2.7_2.7.1-3 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1ubuntu2 libselinux1_3.0-1build2 libsemanage-common_3.0-1build2 libsemanage1_3.0-1build2 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-5ubuntu2 libsqlite3-0_3.31.1-5 libss2_1.45.6-1ubuntu1 libssh-4_0.9.4-1ubuntu1 libssl1.1_1.1.1f-1ubuntu2 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-2ubuntu1 libsub-override-perl_0.09-2 libsystemd0_245.5-3ubuntu1 libtasn1-6_4.16.0-2 libtbb2_2020.2-2 libtcl8.6_8.6.10+dfsg-1 libtiff5_4.1.0+git191117-2build1 libtinfo6_6.2-1 libtk8.6_8.6.10-1 libtool_2.4.6-14 libtsan0_10.1.0-2ubuntu1 libubsan1_10.1.0-2ubuntu1 libuchardet0_0.0.6-3build1 libudev1_245.5-3ubuntu1 libunistring2_0.9.10-2 libuuid1_2.35.1-5ubuntu2 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libwind0-heimdal_7.7.0+dfsg-2 libx11-6_2:1.6.9-2ubuntu1 libx11-data_2:1.6.9-2ubuntu1 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.14-2 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxft2_2.3.3-0ubuntu1 libxml2_2.9.10+dfsg-5 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libyaml-0-2_0.2.2-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.0-29.33 lockfile-progs_0.1.18 login_1:4.8.1-1ubuntu5 logsave_1.45.6-1ubuntu1 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.3-1 man-db_2.9.1-1 mash_2.2.2+dfsg-1build2 mawk_1.3.4.20200120-2 mime-support_3.64ubuntu1 mount_2.35.1-5ubuntu2 mummer_3.23+dfsg-5 ncurses-base_6.2-1 ncurses-bin_6.2-1 node-jquery_3.5.1+dfsg-3 openssl_1.1.1f-1ubuntu2 optipng_0.7.7-1 passwd_1:4.8.1-1ubuntu5 patch_2.7.6-6 perl_5.30.2-1 perl-base_5.30.2-1 perl-modules-5.30_5.30.2-1 pinentry-curses_1.1.0-3build1 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.16-4ubuntu1 python-matplotlib-data_3.1.2-1ubuntu4 python3_3.8.2-0ubuntu2 python3-all_3.8.2-0ubuntu2 python3-all-dev_3.8.2-0ubuntu2 python3-biopython_1.76+dfsg-2 python3-bs4_4.9.0-2 python3-cycler_0.10.0-3 python3-dateutil_2.8.1-4 python3-dendropy_4.4.0-2 python3-dev_3.8.2-0ubuntu2 python3-distutils_3.8.3-2 python3-kiwisolver_1.0.1-3build1 python3-lib2to3_3.8.3-2 python3-matplotlib_3.1.2-1ubuntu4 python3-minimal_3.8.2-0ubuntu2 python3-nose_1.3.7-5 python3-numpy_1:1.18.4-1 python3-pil_7.0.0-4build1 python3-pkg-resources_46.1.3-1 python3-pymummer_0.10.3-2 python3-pyparsing_2.4.7-1 python3-pysam_0.15.4+ds-3 python3-reportlab_3.5.34-1ubuntu1 python3-reportlab-accel_3.5.34-1ubuntu1 python3-setuptools_46.1.3-1 python3-six_1.14.0-3 python3-soupsieve_2.0-1 python3-tk_3.8.3-2 python3.8_3.8.3-1 python3.8-dev_3.8.3-1 python3.8-minimal_3.8.3-1 rake_13.0.1-4 readline-common_8.0-4 ruby_1:2.7+1 ruby-asciidoctor_2.0.10-2 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-1 ruby-test-unit_3.3.5-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.1-3 rubygems-integration_1.16 samtools_1.10-3 sbuild-build-depends-ariba-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 systemd_245.5-3ubuntu1 systemd-sysv_245.5-3ubuntu1 systemd-timesyncd_245.5-3ubuntu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tk8.6-blt2.5_2.5.3+dfsg-4 ttf-bitstream-vera_1.10-8 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.02.11.2 ucf_3.0041 util-linux_2.35.1-5ubuntu2 x11-common_1:7.7+19ubuntu14 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Mar 24 15:15:26 2020 UTC gpgv: using RSA key E7729BFFBE85400FEEEE23B178D7DEFB9AD59AF1 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ariba_2.14.4+ds-2.1.dsc dpkg-source: info: extracting ariba in ariba-2.14.4+ds dpkg-source: info: unpacking ariba_2.14.4+ds.orig.tar.xz dpkg-source: info: unpacking ariba_2.14.4+ds-2.1.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 Check disc space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=4 HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=buildd PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-19212893 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19212893 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19212893 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package ariba dpkg-buildpackage: info: source version 2.14.4+ds-2.1 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/ariba-2.14.4+ds' rm -rf /<>/ariba-2.14.4+ds/debian/man dh_auto_clean -- I: pybuild base:217: python3.8 setup.py clean running clean removing '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build' (and everything under it) 'build/bdist.linux-x86_64' does not exist -- can't clean it 'build/scripts-3.8' does not exist -- can't clean it make[1]: Leaving directory '/<>/ariba-2.14.4+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:217: python3.8 setup.py config running config dh_auto_build -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py build running build running build_py creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/refdata_query.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/ref_seq_chooser.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/histogram.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/aln_to_metadata.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/card_record.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/read_filter.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/read_store.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/pubmlst_getter.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/summary.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/cluster.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/sequence_variant.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/ref_genes_getter.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/sequence_metadata.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/versions.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/reference_data.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/link.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/report_filter.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/assembly_variants.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/cdhit.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/megares_data_finder.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/common.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/ref_preparer.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/scaffold_graph.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/__init__.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/mic_plotter.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/mlst_reporter.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/samtools_variants.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/external_progs.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/megares_zip_parser.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/flag.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/report_flag_expander.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/assembly.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/mapping.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/assembly_compare.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/summary_cluster_variant.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/summary_sample.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/vfdb_parser.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/bam_parse.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/tb.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/summary_cluster.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/mlst_profile.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/clusters.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/faidx.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/pubmlst_ref_preparer.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba copying ariba/report.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/pubmlstget.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/summary.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/version.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/micplot.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/getref.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/aln2meta.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/prepareref_tb.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/__init__.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/expandflag.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/refquery.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/pubmlstspecies.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/flag.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/run.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/prepareref.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks copying ariba/tasks/reportfilter.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/mlst_reporter_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/ref_seq_chooser_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/ref_preparer_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/read_filter_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/mapping_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/summary_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/pubmlst_getter_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/faidx_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/samtools_variants_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/clusters_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/ref_genes_getter_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/megares_data_finder_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/cdhit_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/vfdb_parser_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/mic_plotter_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/summary_cluster_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/report_filter_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/pubmlst_ref_preparer_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/card_record_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/histogram_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/reference_data_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/assembly_variants_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/__init__.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/sequence_variant_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/common_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/flag_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/versions_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/megares_zip_parser_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/read_store_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/link_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/summary_cluster_variant_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/assembly_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/tb_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/mlst_profile_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/ncbi_getter_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/bam_parse_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/aln_to_metadata_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/sequence_metadata_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/scaffold_graph_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/external_progs_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/summary_sample_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/assembly_compare_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/report_flag_expander_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/test_refdata_query.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests copying ariba/tests/cluster_test.py -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data copying ariba/test_run_data/metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_seqs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.json -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.json -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.fa.gz -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.gb -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.json -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.rename -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.out -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.1 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_fasta_file.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_clean.in -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_report.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_getter.dbases.xml -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_rename_file.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.2 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.profile.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_write_report.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_mic_file.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.2.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_rename_sequences.out -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.in -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.expected.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.2.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_long.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_fofn -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.params.json -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_short.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/dummy.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_good.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.out.csv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_data_info_file -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.3 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_ok.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.in -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.1.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.out -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_bad.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_init.fofn -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.read_store -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.info.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.rename_info -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_write_files creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 creating /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 -> /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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-x86_64-3.8 creating build/temp.linux-x86_64-3.8/ariba creating build/temp.linux-x86_64-3.8/ariba/ext x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/ariba-2.14.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.8 -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-x86_64-3.8/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); | ~~~~~~^~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/ariba-2.14.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/ariba/ext/minimap_ariba.o -o /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/minimap_ariba.cpython-38-x86_64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/ariba-2.14.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-x86_64-3.8/ariba/ext/fml-asm_ariba.o x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/ariba-2.14.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/ariba/ext/fml-asm_ariba.o -o /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/fermilite_ariba.cpython-38-x86_64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension x86_64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fdebug-prefix-map=/<>/ariba-2.14.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.8 -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-x86_64-3.8/ariba/ext/vcfcall_ariba.o x86_64-linux-gnu-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>/ariba-2.14.4+ds=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.8/ariba/ext/vcfcall_ariba.o -o /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/vcfcall_ariba.cpython-38-x86_64-linux-gnu.so running build_scripts creating build/scripts-3.8 copying and adjusting scripts/ariba -> build/scripts-3.8 changing mode of build/scripts-3.8/ariba from 644 to 755 dh_auto_test -O--buildsystem=pybuild I: pybuild base:217: cd /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build; python3.8 -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 /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam' [E::idx_find_and_load] Could not retrieve index file for '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 '/<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_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 111.804s 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:217: /usr/bin/python3 setup.py install --root /<>/ariba-2.14.4+ds/debian/ariba running install running build running build_py running build_ext running build_scripts running install_lib creating /<>/ariba-2.14.4+ds/debian/ariba/usr creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8 creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/vcfcall_ariba.cpython-38-x86_64-linux-gnu.so -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/minimap_ariba.cpython-38-x86_64-linux-gnu.so -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/refdata_query.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/ref_seq_chooser.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/histogram.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/refdata_query.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/reference_data.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/mapping.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/summary_cluster_variant.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/pubmlst_getter.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/summary_sample.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/mlst_reporter.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/read_filter.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/vfdb_parser.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/versions.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/card_record.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/external_progs.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/scaffold_graph.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/report_flag_expander.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/common.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/bam_parse.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/__init__.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/link.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/megares_data_finder.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/cluster.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/flag.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/sequence_metadata.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/summary_cluster.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/ref_seq_chooser.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/pubmlst_ref_preparer.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/mlst_profile.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/report.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/cdhit.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/assembly_variants.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/sequence_variant.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/megares_zip_parser.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/histogram.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/samtools_variants.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/read_store.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/clusters.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/aln_to_metadata.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/mic_plotter.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/ref_genes_getter.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/tb.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/report_filter.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/faidx.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/assembly_compare.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/assembly.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/ref_preparer.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__pycache__/summary.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/aln_to_metadata.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/card_record.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/read_filter.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/read_store.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/pubmlst_getter.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/summary.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/cluster.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/sequence_variant.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/ref_genes_getter.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/sequence_metadata.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/versions.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/reference_data.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/link.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/report_filter.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/assembly_variants.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/cdhit.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/megares_data_finder.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/common.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/ref_preparer.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/scaffold_graph.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/__init__.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/mic_plotter.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/mlst_reporter.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/samtools_variants.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/external_progs.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/pubmlstget.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/prepareref_tb.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/version.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/getref.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/prepareref.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/__init__.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/flag.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/micplot.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/refquery.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/aln2meta.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/pubmlstget.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/pubmlstspecies.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/run.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/reportfilter.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/expandflag.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__pycache__/summary.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/summary.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/version.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/micplot.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/getref.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/aln2meta.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/prepareref_tb.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/__init__.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/expandflag.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/refquery.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/pubmlstspecies.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/flag.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/run.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/prepareref.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tasks/reportfilter.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/test_run_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data/metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/test_run_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/test_run_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/test_run_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data/ref_seqs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/test_run_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/test_run_data/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/test_run_data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data/panel.20190102.json -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data/panel.20181221.json -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data/panel.20190102.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data/NC_000962.3.fa.gz -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data/NC_000962.3.gb -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data/panel.20181115.json -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data/panel.20181221.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb_data/panel.20181115.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb_data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/megares_zip_parser.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/flag.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/report_flag_expander.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/assembly.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/mapping.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/assembly_compare.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/summary_cluster_variant.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/summary_sample.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/vfdb_parser.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/bam_parse.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tb.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/summary_cluster.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/mlst_profile.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/clusters.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/faidx.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/pubmlst_ref_preparer.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/report.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/mlst_reporter_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/ref_seq_chooser_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/ref_preparer_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/read_filter_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/mapping_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/summary_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/reference_data_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/read_filter_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/cdhit_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/mlst_profile_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/mapping_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/versions_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/summary_sample_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/ref_genes_getter_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/assembly_variants_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/ref_preparer_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/clusters_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/cluster_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/tb_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/samtools_variants_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/summary_cluster_variant_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/__init__.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/test_refdata_query.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/sequence_metadata_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/report_filter_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/pubmlst_getter_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/link_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/card_record_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/pubmlst_ref_preparer_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/assembly_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/scaffold_graph_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/flag_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/mlst_reporter_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/megares_zip_parser_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/ncbi_getter_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/faidx_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/ref_seq_chooser_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/bam_parse_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/external_progs_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/mic_plotter_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/common_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/report_flag_expander_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/megares_data_finder_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/vfdb_parser_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/histogram_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/summary_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/summary_cluster_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/aln_to_metadata_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/sequence_variant_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/assembly_compare_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__pycache__/read_store_test.cpython-38.pyc -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__pycache__ copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/pubmlst_getter_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/faidx_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.in.3.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/report_filter_test_load_report_good.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/graph_test_write_all_links_to_file.out -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_fix_out.rename -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_fix_out.removed.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_sequence.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/test_common_cat_files.out -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/test_common_cat_files.in.1 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_fasta_file.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_dummy_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_clean.in -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_check_not_gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads.no_link_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/report_flag_expander.run.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads.no_link_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_report.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/pubmlst_getter.dbases.xml -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_init_fails.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.profile.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_run_fermilite.reads.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_fix_in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_sequence_type.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_rename_file.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/test_common_cat_files.in.2 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_dummy_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_count_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_profile_test.profile.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_init_ok.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_profile_test.init.profile.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/report_filter_test_write_report.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_load_annotations.csv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_compress_and_index_file.in -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_load_mic_file.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/00.info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref/00.rename_info -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_test_whole_run.in.2.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/tb_genbank_to_gene_coords.gb -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_test_whole_run.in.1.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_rename_sequences.out -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_dummy_db.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_test_load_input_files.2.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_sequence_type.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads.make_link_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_test_run.in.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/report_flag_expander.run.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_sort_file.in -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/report_filter_test_run.expected.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_fix_out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_run.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads.make_link_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_to_matrix.2.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_fake_run.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_load_summary_file.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_check_too_long.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_sequence.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_init_fails.empty.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_init_ok.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_test_load_fofn -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_init_ok.params.json -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_parse.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.ref.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_check_too_short.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_sample_test_var_groups.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_rename_sequences.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/tb_report_to_resistance_dict.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/link_test_init.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_refdata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/report_filter_test_load_report_bad.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_test_load_input_files.1.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_dummy_db.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/dummy.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/report_filter_test_init_good.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_refdata.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_test_whole_run.out.csv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refdata_query_prepareref.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_load_data_info_file -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_parse.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/report_filter_test_run.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_init_fails.empty.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_count_reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/test_common_cat_files.in.3 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_init_ok.rename.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/pubmlst_rename_seqs.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.vcf -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_check_ok.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_get_reads.in -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_remove_bad_genes.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_test_write_distance_matrix.distances -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_to_matrix.1.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/refcheck_test_fix_out.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_store_test_sort_file.out -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/vfdb_parser_test_run.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/report_filter_test_init_bad.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_test_init.fofn -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/read_filter_test_run.in.read_store -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data creating /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/clusters_cat_genes_match_ref.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/summary_sample_test_load_file.in.tsv -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/data copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/samtools_variants_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/clusters_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/ref_genes_getter_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/megares_data_finder_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/cdhit_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/vfdb_parser_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/mic_plotter_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/summary_cluster_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/report_filter_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/card_record_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/histogram_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/reference_data_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_variants_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/__init__.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/sequence_variant_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/common_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/flag_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/versions_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/megares_zip_parser_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/read_store_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/link_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/summary_cluster_variant_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/tb_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/mlst_profile_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/ncbi_getter_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/bam_parse_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/aln_to_metadata_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/sequence_metadata_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/scaffold_graph_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/external_progs_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/summary_sample_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/assembly_compare_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/report_flag_expander_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/test_refdata_query.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/ariba/tests/cluster_test.py -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests copying /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/fermilite_ariba.cpython-38-x86_64-linux-gnu.so -> /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/refdata_query.py to refdata_query.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/histogram.py to histogram.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/card_record.py to card_record.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/read_filter.py to read_filter.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/read_store.py to read_store.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/pubmlst_getter.py to pubmlst_getter.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/summary.py to summary.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/cluster.py to cluster.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/versions.py to versions.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/reference_data.py to reference_data.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/link.py to link.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/report_filter.py to report_filter.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/cdhit.py to cdhit.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/common.py to common.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/samtools_variants.py to samtools_variants.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/external_progs.py to external_progs.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/test.py to test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/summary.py to summary.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/version.py to version.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/micplot.py to micplot.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/getref.py to getref.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/prepareref_tb.py to prepareref_tb.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/refquery.py to refquery.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/pubmlstspecies.py to pubmlstspecies.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/flag.py to flag.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/run.py to run.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/prepareref.py to prepareref.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/flag.py to flag.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/assembly.py to assembly.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/mapping.py to mapping.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/summary_sample.py to summary_sample.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/bam_parse.py to bam_parse.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tb.py to tb.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/mlst_profile.py to mlst_profile.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/clusters.py to clusters.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/faidx.py to faidx.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/report.py to report.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/mlst_reporter_test.py to mlst_reporter_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/ref_seq_chooser_test.py to ref_seq_chooser_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/ref_preparer_test.py to ref_preparer_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/read_filter_test.py to read_filter_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/mapping_test.py to mapping_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/summary_test.py to summary_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/pubmlst_getter_test.py to pubmlst_getter_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/faidx_test.py to faidx_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/samtools_variants_test.py to samtools_variants_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/clusters_test.py to clusters_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/ref_genes_getter_test.py to ref_genes_getter_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/megares_data_finder_test.py to megares_data_finder_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/cdhit_test.py to cdhit_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/vfdb_parser_test.py to vfdb_parser_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/mic_plotter_test.py to mic_plotter_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/summary_cluster_test.py to summary_cluster_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/report_filter_test.py to report_filter_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py to pubmlst_ref_preparer_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/card_record_test.py to card_record_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/histogram_test.py to histogram_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/reference_data_test.py to reference_data_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/assembly_variants_test.py to assembly_variants_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/__init__.py to __init__.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/sequence_variant_test.py to sequence_variant_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/common_test.py to common_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/flag_test.py to flag_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/versions_test.py to versions_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/megares_zip_parser_test.py to megares_zip_parser_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/read_store_test.py to read_store_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/link_test.py to link_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/summary_cluster_variant_test.py to summary_cluster_variant_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/assembly_test.py to assembly_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/tb_test.py to tb_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/mlst_profile_test.py to mlst_profile_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/ncbi_getter_test.py to ncbi_getter_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/bam_parse_test.py to bam_parse_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/aln_to_metadata_test.py to aln_to_metadata_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/sequence_metadata_test.py to sequence_metadata_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/scaffold_graph_test.py to scaffold_graph_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/external_progs_test.py to external_progs_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/summary_sample_test.py to summary_sample_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/assembly_compare_test.py to assembly_compare_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/report_flag_expander_test.py to report_flag_expander_test.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/test_refdata_query.py to test_refdata_query.cpython-38.pyc byte-compiling /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba/tests/cluster_test.py to cluster_test.cpython-38.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 /<>/ariba-2.14.4+ds/debian/ariba/usr/lib/python3.8/dist-packages/ariba-2.14.4.egg-info Skipping SOURCES.txt running install_scripts creating /<>/ariba-2.14.4+ds/debian/ariba/usr/bin copying build/scripts-3.8/ariba -> /<>/ariba-2.14.4+ds/debian/ariba/usr/bin changing mode of /<>/ariba-2.14.4+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 '/<>/ariba-2.14.4+ds' mkdir -p /<>/ariba-2.14.4+ds/debian/man asciidoctor -a docdate='' -b manpage -o /<>/ariba-2.14.4+ds/debian/man/ariba.1 /<>/ariba-2.14.4+ds/debian/ariba.1.adoc dh_installman -- make[1]: Leaving directory '/<>/ariba-2.14.4+ds' dh_python3 -O--buildsystem=pybuild dh_installinit -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 -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ariba/usr/lib/python3/dist-packages/vcfcall_ariba.cpython-38-x86_64-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 INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing ariba-dbgsym (in debian/.debhelper/ariba/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing ariba (in debian/ariba); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/ariba/dbgsym-root/DEBIAN/control, package ariba-dbgsym, directory debian/.debhelper/ariba/dbgsym-root dpkg-deb: building package 'ariba-dbgsym' in 'debian/.debhelper/scratch-space/build-ariba/ariba-dbgsym_2.14.4+ds-2.1_amd64.deb'. Renaming ariba-dbgsym_2.14.4+ds-2.1_amd64.deb to ariba-dbgsym_2.14.4+ds-2.1_amd64.ddeb pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/ariba/DEBIAN/control, package ariba, directory debian/ariba pkgstripfiles: Truncating usr/share/doc/ariba/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package ariba ... pkgstripfiles: No PNG files. dpkg-deb: building package 'ariba' in '../ariba_2.14.4+ds-2.1_amd64.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary -mLaunchpad Build Daemon >../ariba_2.14.4+ds-2.1_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200521-1558 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ ariba_2.14.4+ds-2.1_amd64.changes: ---------------------------------- Format: 1.8 Date: Tue, 24 Mar 2020 11:14:59 -0400 Source: ariba Binary: ariba Architecture: amd64 Version: 2.14.4+ds-2.1 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Scott Kitterman Description: ariba - Antibiotic Resistance Identification By Assembly Closes: 951944 Changes: ariba (2.14.4+ds-2.1) unstable; urgency=medium . * Non-maintainer upload. * Build for all supported python3 versions to fix test failures in complex Python environments and ease python3 transitions (Closes: #951944) Checksums-Sha1: 38e9ea175cc345dc9de49f0bd9915caf928ca1f7 394012 ariba-dbgsym_2.14.4+ds-2.1_amd64.ddeb 37534adeeb1ad8bcc25348935fe194ce7e7b348c 9788 ariba_2.14.4+ds-2.1_amd64.buildinfo 60bbcea1f2993eb6af683e5573e73484f839145c 1944208 ariba_2.14.4+ds-2.1_amd64.deb Checksums-Sha256: 9832ba019fc9b4c6497c31ebe56c65f9fc0dc11cb6dd9763ab827793f3148a0b 394012 ariba-dbgsym_2.14.4+ds-2.1_amd64.ddeb a8de783998e0edc6c85679bf7ac9568fca4a6e4d30e66922bbb4f8062a40c98a 9788 ariba_2.14.4+ds-2.1_amd64.buildinfo 17d406f8f4de262e7792fc6f15221aa10b3a1a3687ed32f8900183d476d367c7 1944208 ariba_2.14.4+ds-2.1_amd64.deb Files: 55e5ecfa2464303436fa667a2bbbfa8c 394012 debug optional ariba-dbgsym_2.14.4+ds-2.1_amd64.ddeb eb9ceb38ae84caddfbc271b4856586c9 9788 science optional ariba_2.14.4+ds-2.1_amd64.buildinfo f2d94fa209acad6eaaa5819ab92bac24 1944208 science optional ariba_2.14.4+ds-2.1_amd64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ ariba_2.14.4+ds-2.1_amd64.deb ----------------------------- new debian package, version 2.0. size 1944208 bytes: control archive=17868 bytes. 1128 bytes, 17 lines control 91134 bytes, 756 lines md5sums 235 bytes, 12 lines * postinst #!/bin/sh 384 bytes, 12 lines * prerm #!/bin/sh Package: ariba Version: 2.14.4+ds-2.1 Architecture: amd64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 20454 Depends: fastaq (>= 3.12.0), python3 (<< 3.9), python3 (>= 3.8~), python3-biopython, python3-bs4, python3-dendropy, python3-matplotlib, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3:any, libc6 (>= 2.14), libfml0 (>= 0.1-4~), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2 (>= 2.1.0), cd-hit, mash, mummer, python3-tk Section: science Priority: optional Homepage: https://github.com/sanger-pathogens/ariba Description: Antibiotic Resistance Identification By Assembly ARIBA is a tool that identifies antibiotic resistance genes by running local assemblies. The input is a FASTA file of reference genes and paired sequencing reads. ARIBA reports which of the reference genes were found, plus detailed information on the quality of the assemblies and any variants between the sequencing reads and the reference genes. drwxr-xr-x root/root 0 2020-03-24 15:14 ./ drwxr-xr-x root/root 0 2020-03-24 15:14 ./usr/ drwxr-xr-x root/root 0 2020-03-24 15:14 ./usr/bin/ -rwxr-xr-x root/root 26193 2020-03-24 15:14 ./usr/bin/ariba drwxr-xr-x root/root 0 2020-03-24 15:14 ./usr/lib/ drwxr-xr-x root/root 0 2020-03-24 15:14 ./usr/lib/python3/ drwxr-xr-x root/root 0 2020-03-24 15:14 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2020-03-24 15:14 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/ -rw-r--r-- root/root 519 2020-03-24 15:14 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/PKG-INFO -rw-r--r-- root/root 1 2020-03-24 15:14 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2020-03-24 15:14 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/requires.txt -rw-r--r-- root/root 50 2020-03-24 15:14 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/top_level.txt drwxr-xr-x root/root 0 2020-03-24 15:14 ./usr/lib/python3/dist-packages/ariba/ -rw-r--r-- root/root 1063 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/__init__.py -rw-r--r-- root/root 10940 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/aln_to_metadata.py -rw-r--r-- root/root 15099 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/assembly.py -rw-r--r-- root/root 16416 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/assembly_compare.py -rw-r--r-- root/root 15177 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/assembly_variants.py -rw-r--r-- root/root 3586 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/bam_parse.py -rw-r--r-- root/root 3328 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/card_record.py -rw-r--r-- root/root 6274 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/cdhit.py -rw-r--r-- root/root 19456 2019-09-24 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Build-Time: 160 Distribution: groovy-proposed Host Architecture: amd64 Install-Time: 49 Job: ariba_2.14.4+ds-2.1.dsc Machine Architecture: amd64 Package: ariba Package-Time: 211 Source-Version: 2.14.4+ds-2.1 Space: 77296 Status: successful Version: 2.14.4+ds-2.1 -------------------------------------------------------------------------------- Finished at 20200521-1558 Build needed 00:03:31, 77296k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=amd64 PACKAGEBUILD-19212893 Scanning for processes to kill in build PACKAGEBUILD-19212893