https://launchpad.net/ubuntu/+source/ariba/2.14.4+ds-2build1/+build/18608256 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-060 4.4.0-171-generic #200-Ubuntu SMP Tue Dec 3 11:07:23 UTC 2019 aarch64 Buildd toolchain package versions: launchpad-buildd_186 python-lpbuildd_186 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_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 25 Jan 04:58:59 ntpdate[1958]: adjust time server 10.211.37.1 offset -0.001784 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18608256 --image-type chroot /home/buildd/filecache-default/9d93b4075e16ce7cfbdf01f21507152b0a173b17 Creating target for build PACKAGEBUILD-18608256 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18608256 Starting target for build PACKAGEBUILD-18608256 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18608256 'deb http://ftpmaster.internal/ubuntu focal main universe' 'deb http://ftpmaster.internal/ubuntu focal-security main universe' 'deb http://ftpmaster.internal/ubuntu focal-updates main universe' 'deb http://ftpmaster.internal/ubuntu focal-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-18608256 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18608256 Updating target for build PACKAGEBUILD-18608256 Get:1 http://ftpmaster.internal/ubuntu focal InRelease [255 kB] Get:2 http://ftpmaster.internal/ubuntu focal-security InRelease [79.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal-updates InRelease [79.7 kB] Get:4 http://ftpmaster.internal/ubuntu focal-proposed InRelease [255 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main arm64 Packages [940 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main Translation-en [501 kB] Get:7 http://ftpmaster.internal/ubuntu focal/universe arm64 Packages [8398 kB] Get:8 http://ftpmaster.internal/ubuntu focal/universe Translation-en [5138 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 Packages [90.5 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main Translation-en [39.3 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 Packages [409 kB] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/universe Translation-en [213 kB] Fetched 16.4 MB in 6s (2548 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libctf-nobfd0 libctf0 libffi7 libhogweed5 libisl22 libnettle7 libperl5.30 perl-modules-5.30 The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-aarch64-linux-gnu binutils-common bsdutils bzip2 cpp-9 debianutils e2fsprogs fdisk g++-9 gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip hostname libacl1 libapparmor1 libapt-pkg5.90 libasan5 libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libcryptsetup12 libdebconfclient0 libdevmapper1.02.1 libext2fs2 libfdisk1 libgcc-9-dev libgcc1 libgcrypt20 libgnutls30 libgomp1 libgpg-error0 libitm1 libjson-c4 libkmod2 liblockfile-bin liblockfile1 liblsan0 liblz4-1 libmount1 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsmartcols1 libsqlite3-0 libss2 libssl1.1 libstdc++-9-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan0 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev login logsave lsb-base mount ncurses-base ncurses-bin openssl passwd perl perl-base sensible-utils systemd systemd-sysv sysvinit-utils util-linux 104 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. Need to get 58.3 MB of archives. After this operation, 40.0 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu focal/main arm64 libc6-dev arm64 2.30-0ubuntu3 [2091 kB] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 libc-dev-bin arm64 2.30-0ubuntu3 [64.1 kB] Get:3 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 linux-libc-dev arm64 5.4.0-12.15 [1084 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main arm64 libisl22 arm64 0.22-2 [536 kB] Get:5 http://ftpmaster.internal/ubuntu focal/main arm64 libcc1-0 arm64 9.2.1-25ubuntu1 [37.1 kB] Get:6 http://ftpmaster.internal/ubuntu focal/main arm64 libctf-nobfd0 arm64 2.33.90.20200122-1ubuntu2 [43.4 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main arm64 libctf0 arm64 2.33.90.20200122-1ubuntu2 [43.0 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main arm64 binutils-aarch64-linux-gnu arm64 2.33.90.20200122-1ubuntu2 [1988 kB] Get:9 http://ftpmaster.internal/ubuntu focal/main arm64 libbinutils arm64 2.33.90.20200122-1ubuntu2 [473 kB] Get:10 http://ftpmaster.internal/ubuntu focal/main arm64 binutils-common arm64 2.33.90.20200122-1ubuntu2 [206 kB] Get:11 http://ftpmaster.internal/ubuntu focal/main arm64 binutils arm64 2.33.90.20200122-1ubuntu2 [3356 B] Get:12 http://ftpmaster.internal/ubuntu focal/main arm64 gcc-9-base arm64 9.2.1-25ubuntu1 [19.2 kB] Get:13 http://ftpmaster.internal/ubuntu focal/main arm64 libgcc1 arm64 1:9.2.1-25ubuntu1 [34.3 kB] Get:14 http://ftpmaster.internal/ubuntu focal/main arm64 libgomp1 arm64 9.2.1-25ubuntu1 [80.6 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main arm64 libitm1 arm64 9.2.1-25ubuntu1 [25.0 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main arm64 libatomic1 arm64 9.2.1-25ubuntu1 [9168 B] Get:17 http://ftpmaster.internal/ubuntu focal/main arm64 libasan5 arm64 9.2.1-25ubuntu1 [365 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main arm64 liblsan0 arm64 9.2.1-25ubuntu1 [126 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main arm64 libtsan0 arm64 9.2.1-25ubuntu1 [284 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main arm64 libubsan1 arm64 9.2.1-25ubuntu1 [121 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main arm64 g++-9 arm64 9.2.1-25ubuntu1 [6811 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main arm64 libstdc++-9-dev arm64 9.2.1-25ubuntu1 [1675 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main arm64 libgcc-9-dev arm64 9.2.1-25ubuntu1 [909 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main arm64 gcc-9 arm64 9.2.1-25ubuntu1 [6675 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main arm64 cpp-9 arm64 9.2.1-25ubuntu1 [5960 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main arm64 libstdc++6 arm64 9.2.1-25ubuntu1 [466 kB] Get:27 http://ftpmaster.internal/ubuntu focal/main arm64 libc6 arm64 2.30-0ubuntu3 [2273 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main arm64 base-files arm64 11ubuntu2 [60.0 kB] Get:29 http://ftpmaster.internal/ubuntu focal/main arm64 debianutils arm64 4.9.1 [85.6 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main arm64 bash arm64 5.0-5ubuntu1 [603 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main arm64 bsdutils arm64 1:2.34-0.1ubuntu5 [60.7 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main arm64 gzip arm64 1.10-0ubuntu4 [93.0 kB] Get:33 http://ftpmaster.internal/ubuntu focal/main arm64 hostname arm64 3.23 [11.1 kB] Get:34 http://ftpmaster.internal/ubuntu focal/main arm64 login arm64 1:4.8-1ubuntu1 [218 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main arm64 ncurses-bin arm64 6.1+20191019-1ubuntu1 [166 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main arm64 perl-modules-5.30 all 5.30.0-9 [2739 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main arm64 libperl5.30 arm64 5.30.0-9 [3764 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main arm64 perl arm64 5.30.0-9 [224 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main arm64 perl-base arm64 5.30.0-9 [1389 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main arm64 bzip2 arm64 1.0.8-2 [33.0 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main arm64 libbz2-1.0 arm64 1.0.8-2 [32.9 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main arm64 libblkid1 arm64 2.34-0.1ubuntu5 [129 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main arm64 libuuid1 arm64 2.34-0.1ubuntu5 [19.9 kB] Get:44 http://ftpmaster.internal/ubuntu focal/main arm64 libfdisk1 arm64 2.34-0.1ubuntu5 [160 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main arm64 libpcre2-8-0 arm64 10.34-7 [170 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main arm64 libselinux1 arm64 3.0-1 [64.8 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main arm64 libmount1 arm64 2.34-0.1ubuntu5 [140 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main arm64 libncurses6 arm64 6.1+20191019-1ubuntu1 [91.8 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main arm64 libtinfo6 arm64 6.1+20191019-1ubuntu1 [80.4 kB] Get:50 http://ftpmaster.internal/ubuntu focal/main arm64 libncursesw6 arm64 6.1+20191019-1ubuntu1 [120 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main arm64 libsmartcols1 arm64 2.34-0.1ubuntu5 [93.4 kB] Get:52 http://ftpmaster.internal/ubuntu focal/main arm64 fdisk arm64 2.34-0.1ubuntu5 [114 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main arm64 util-linux arm64 2.34-0.1ubuntu5 [982 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main arm64 libdebconfclient0 arm64 0.250ubuntu2 [6260 B] Get:55 http://ftpmaster.internal/ubuntu focal/main arm64 base-passwd arm64 3.5.47 [47.0 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main arm64 libc-bin arm64 2.30-0ubuntu3 [502 kB] Get:57 http://ftpmaster.internal/ubuntu focal/main arm64 ncurses-base all 6.1+20191019-1ubuntu1 [17.9 kB] Get:58 http://ftpmaster.internal/ubuntu focal/main arm64 lsb-base all 11.1.0ubuntu2 [12.1 kB] Get:59 http://ftpmaster.internal/ubuntu focal/main arm64 sysvinit-utils arm64 2.96-1ubuntu1 [20.5 kB] Get:60 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libgpg-error0 arm64 1.36-7build1 [54.9 kB] Get:61 http://ftpmaster.internal/ubuntu focal/main arm64 libgcrypt20 arm64 1.8.5-3ubuntu1 [350 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main arm64 liblz4-1 arm64 1.9.2-2 [52.7 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main arm64 systemd-sysv arm64 244.1-0ubuntu2 [9364 B] Get:64 http://ftpmaster.internal/ubuntu focal/main arm64 libacl1 arm64 2.2.53-5ubuntu1 [17.7 kB] Get:65 http://ftpmaster.internal/ubuntu focal/main arm64 libapparmor1 arm64 2.13.3-7ubuntu1 [33.2 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main arm64 libaudit-common all 1:2.8.5-2ubuntu5 [4076 B] Get:67 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libcap-ng0 arm64 0.7.9-2.1build1 [10.5 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main arm64 libaudit1 arm64 1:2.8.5-2ubuntu5 [38.4 kB] Get:69 http://ftpmaster.internal/ubuntu focal/main arm64 libcap2 arm64 1:2.27-1 [13.9 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main arm64 libudev1 arm64 244.1-0ubuntu2 [70.5 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main arm64 libdevmapper1.02.1 arm64 2:1.02.155-2ubuntu7 [111 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main arm64 libjson-c4 arm64 0.13.1+dfsg-6 [28.0 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main arm64 libssl1.1 arm64 1.1.1d-2ubuntu3 [1153 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main arm64 libcryptsetup12 arm64 2:2.2.2-1ubuntu1 [166 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main arm64 libnettle7 arm64 3.5.1+really3.5.1-2 [124 kB] Get:76 http://ftpmaster.internal/ubuntu focal/main arm64 libhogweed5 arm64 3.5.1+really3.5.1-2 [134 kB] Get:77 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libffi7 arm64 3.3-3 [17.1 kB] Get:78 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libp11-kit0 arm64 0.23.18.1-2build1 [176 kB] Get:79 http://ftpmaster.internal/ubuntu focal/main arm64 libtasn1-6 arm64 4.15.0-2 [36.3 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main arm64 libgnutls30 arm64 3.6.11.1-2ubuntu2 [720 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main arm64 libkmod2 arm64 26-3ubuntu1 [39.5 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main arm64 libpam0g arm64 1.3.1-5ubuntu4 [53.9 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main arm64 libseccomp2 arm64 2.4.2-2ubuntu2 [39.8 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main arm64 mount arm64 2.34-0.1ubuntu5 [112 kB] Get:85 http://ftpmaster.internal/ubuntu focal/main arm64 systemd arm64 244.1-0ubuntu2 [3384 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main arm64 libsystemd0 arm64 244.1-0ubuntu2 [240 kB] Get:87 http://ftpmaster.internal/ubuntu focal/main arm64 libzstd1 arm64 1.4.4+dfsg-1 [216 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main arm64 libapt-pkg5.90 arm64 1.9.7 [776 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main arm64 gpgv arm64 2.2.17-3ubuntu1 [183 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main arm64 apt arm64 1.9.7 [1229 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main arm64 libpam-modules-bin arm64 1.3.1-5ubuntu4 [35.8 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main arm64 libpam-modules arm64 1.3.1-5ubuntu4 [242 kB] Get:93 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 logsave arm64 1.45.3-4ubuntu3 [9680 B] Get:94 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libext2fs2 arm64 1.45.3-4ubuntu3 [174 kB] Get:95 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 e2fsprogs arm64 1.45.3-4ubuntu3 [502 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main arm64 libattr1 arm64 1:2.4.48-5 [12.5 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main arm64 libpam-runtime all 1.3.1-5ubuntu4 [37.3 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main arm64 libsepol1 arm64 3.0-1 [231 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main arm64 libsemanage-common all 3.0-1 [9880 B] Get:100 http://ftpmaster.internal/ubuntu focal/main arm64 libsemanage1 arm64 3.0-1 [79.6 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main arm64 passwd arm64 1:4.8-1ubuntu1 [771 kB] Get:102 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libcom-err2 arm64 1.45.3-4ubuntu3 [8848 B] Get:103 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libss2 arm64 1.45.3-4ubuntu3 [10.7 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main arm64 sensible-utils all 0.0.12+nmu1 [15.0 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main arm64 libsqlite3-0 arm64 3.30.1-1ubuntu1 [499 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main arm64 openssl arm64 1.1.1d-2ubuntu3 [597 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main arm64 libassuan0 arm64 2.5.3-7ubuntu2 [33.1 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main arm64 gpg arm64 2.2.17-3ubuntu1 [437 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main arm64 gpgconf arm64 2.2.17-3ubuntu1 [117 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main arm64 gpg-agent arm64 2.2.17-3ubuntu1 [216 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main arm64 liblockfile-bin arm64 1.16-1.1 [11.3 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main arm64 liblockfile1 arm64 1.16-1.1 [6440 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 58.3 MB in 2s (28.0 MB/s) (Reading database ... 12731 files and directories currently installed.) Preparing to unpack .../00-libc6-dev_2.30-0ubuntu3_arm64.deb ... Unpacking libc6-dev:arm64 (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../01-libc-dev-bin_2.30-0ubuntu3_arm64.deb ... Unpacking libc-dev-bin (2.30-0ubuntu3) over (2.30-0ubuntu2) ... Preparing to unpack .../02-linux-libc-dev_5.4.0-12.15_arm64.deb ... Unpacking linux-libc-dev:arm64 (5.4.0-12.15) over (5.3.0-18.19) ... Selecting previously unselected package libisl22:arm64. Preparing to unpack .../03-libisl22_0.22-2_arm64.deb ... Unpacking libisl22:arm64 (0.22-2) ... Preparing to unpack .../04-libcc1-0_9.2.1-25ubuntu1_arm64.deb ... Unpacking libcc1-0:arm64 (9.2.1-25ubuntu1) over (9.2.1-9ubuntu2) ... Selecting previously unselected package libctf-nobfd0:arm64. Preparing to unpack .../05-libctf-nobfd0_2.33.90.20200122-1ubuntu2_arm64.deb ... Unpacking libctf-nobfd0:arm64 (2.33.90.20200122-1ubuntu2) ... Selecting previously unselected package libctf0:arm64. 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Setting up libbinutils:arm64 (2.33.90.20200122-1ubuntu2) ... Setting up libc-dev-bin (2.30-0ubuntu3) ... Setting up openssl (1.1.1d-2ubuntu3) ... Setting up libcc1-0:arm64 (9.2.1-25ubuntu1) ... Setting up gpg (2.2.17-3ubuntu1) ... Setting up liblsan0:arm64 (9.2.1-25ubuntu1) ... Setting up libitm1:arm64 (9.2.1-25ubuntu1) ... Setting up libkmod2:arm64 (26-3ubuntu1) ... Setting up libtsan0:arm64 (9.2.1-25ubuntu1) ... Setting up libctf0:arm64 (2.33.90.20200122-1ubuntu2) ... Setting up gpg-agent (2.2.17-3ubuntu1) ... Installing new version of config file /etc/logcheck/ignore.d.server/gpg-agent ... Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket -> /usr/lib/systemd/user/gpg-agent-browser.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket -> /usr/lib/systemd/user/gpg-agent-extra.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket -> /usr/lib/systemd/user/gpg-agent-ssh.socket. Created symlink /etc/systemd/user/sockets.target.wants/gpg-agent.socket -> /usr/lib/systemd/user/gpg-agent.socket. Setting up binutils-aarch64-linux-gnu (2.33.90.20200122-1ubuntu2) ... Setting up e2fsprogs (1.45.3-4ubuntu3) ... Setting up binutils (2.33.90.20200122-1ubuntu2) ... Setting up libgcc-9-dev:arm64 (9.2.1-25ubuntu1) ... Setting up perl (5.30.0-9) ... Setting up cpp-9 (9.2.1-25ubuntu1) ... Setting up libc6-dev:arm64 (2.30-0ubuntu3) ... Setting up libcryptsetup12:arm64 (2:2.2.2-1ubuntu1) ... Setting up gcc-9 (9.2.1-25ubuntu1) ... Setting up libstdc++-9-dev:arm64 (9.2.1-25ubuntu1) ... Setting up systemd (244.1-0ubuntu2) ... Installing new version of config file /etc/dhcp/dhclient-enter-hooks.d/resolved ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... Initializing machine ID from KVM UUID. Setting up g++-9 (9.2.1-25ubuntu1) ... Setting up systemd-sysv (244.1-0ubuntu2) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-18608256 arm64 focal-proposed -c chroot:build-PACKAGEBUILD-18608256 --arch=arm64 --dist=focal-proposed --nolog ariba_2.14.4+ds-2build1.dsc Initiating build PACKAGEBUILD-18608256 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-171-generic #200-Ubuntu SMP Tue Dec 3 11:07:23 UTC 2019 aarch64 sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-060.buildd +==============================================================================+ | ariba 2.14.4+ds-2build1 (arm64) 25 Jan 2020 04:59 | +==============================================================================+ Package: ariba Version: 2.14.4+ds-2build1 Source Version: 2.14.4+ds-2build1 Distribution: focal-proposed Machine Architecture: arm64 Host Architecture: arm64 Build Architecture: arm64 I: NOTICE: Log filtering will replace 'build/ariba-raPQnn/ariba-2.14.4+ds' with '<>' I: NOTICE: Log filtering will replace 'build/ariba-raPQnn' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-18608256/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- ariba_2.14.4+ds-2build1.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-gr8YI5/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-gr8YI5/apt_archive ./ InRelease Get:2 copy:/<>/resolver-gr8YI5/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-gr8YI5/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-gr8YI5/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-gr8YI5/apt_archive ./ Packages [528 B] Fetched 2861 B in 0s (97.8 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 packages were automatically installed and are no longer required: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. 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-gr8YI5/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 (68.9 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 14657 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_arm64.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-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-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-veUZF8/apt_archive/sbuild-build-depends-ariba-dummy.deb'. Ign:1 copy:/<>/resolver-veUZF8/apt_archive ./ InRelease Get:2 copy:/<>/resolver-veUZF8/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-veUZF8/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-veUZF8/apt_archive ./ Sources [363 B] Get:5 copy:/<>/resolver-veUZF8/apt_archive ./ Packages [688 B] Fetched 3170 B in 0s (109 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 packages were automatically installed and are no longer required: libffi6 libhogweed4 libisl21 libnettle6 libperl5.28 perl-modules-5.28 Use 'apt autoremove' to remove them. 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 libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libicu63 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-dev libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl 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 po-debconf python-matplotlib-data python3 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 python3.7 python3.7-minimal python3.8 python3.8-dev python3.8-minimal rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5 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-pyqt4 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 python3.7-venv python3.7-doc binfmt-support python3.8-venv python3.8-doc 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 libgsl23 libgslcblas0 libgssapi-krb5-2 libgssapi3-heimdal libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts3 libhx509-5-heimdal libicu63 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-dev libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev libpython3.8-minimal libpython3.8-stdlib libroken18-heimdal librtmp1 libruby2.5 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl 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 po-debconf python-matplotlib-data python3 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 python3.7 python3.7-minimal python3.8 python3.8-dev python3.8-minimal rake ruby ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-xmlrpc ruby2.5 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 70.6 MB of archives. After this operation, 300 MB of additional disk space will be used. Get:1 copy:/<>/resolver-veUZF8/apt_archive ./ sbuild-build-depends-ariba-dummy 0.invalid.0 [1016 B] Get:2 http://ftpmaster.internal/ubuntu focal/main arm64 liblocale-gettext-perl arm64 1.07-4 [16.7 kB] Get:3 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3.8-minimal arm64 3.8.1-2ubuntu3 [701 kB] Get:4 http://ftpmaster.internal/ubuntu focal/main arm64 libexpat1 arm64 2.2.9-1 [61.3 kB] Get:5 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3.8-minimal arm64 3.8.1-2ubuntu3 [1821 kB] Get:6 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3-minimal arm64 3.8.0-3 [23.4 kB] Get:7 http://ftpmaster.internal/ubuntu focal/main arm64 mime-support all 3.64ubuntu1 [30.6 kB] Get:8 http://ftpmaster.internal/ubuntu focal/main arm64 libmpdec2 arm64 2.4.2-2 [74.0 kB] Get:9 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3.8-stdlib arm64 3.8.1-2ubuntu3 [1643 kB] Get:10 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3.8 arm64 3.8.1-2ubuntu3 [360 kB] Get:11 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3-stdlib arm64 3.8.0-3 [6904 B] Get:12 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3 arm64 3.8.0-3 [47.6 kB] Get:13 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3.7-minimal arm64 3.7.6-1ubuntu2 [547 kB] Get:14 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3.7-minimal arm64 3.7.6-1ubuntu2 [1723 kB] Get:15 http://ftpmaster.internal/ubuntu focal/main arm64 libbsd0 arm64 0.10.0-1 [43.7 kB] Get:16 http://ftpmaster.internal/ubuntu focal/main arm64 bsdmainutils arm64 11.1.2ubuntu2 [175 kB] Get:17 http://ftpmaster.internal/ubuntu focal/main arm64 libuchardet0 arm64 0.0.6-3 [65.0 kB] Get:18 http://ftpmaster.internal/ubuntu focal/main arm64 groff-base arm64 1.22.4-4 [815 kB] Get:19 http://ftpmaster.internal/ubuntu focal/main arm64 libpipeline1 arm64 1.5.2-2 [26.0 kB] Get:20 http://ftpmaster.internal/ubuntu focal/main arm64 man-db arm64 2.9.0-2 [1097 kB] Get:21 http://ftpmaster.internal/ubuntu focal/main arm64 libsigsegv2 arm64 2.12-2 [13.3 kB] Get:22 http://ftpmaster.internal/ubuntu focal/main arm64 gawk arm64 1:5.0.1+dfsg-1 [382 kB] Get:23 http://ftpmaster.internal/ubuntu focal/main arm64 libmagic-mgc arm64 1:5.37-6ubuntu1 [209 kB] Get:24 http://ftpmaster.internal/ubuntu focal/main arm64 libmagic1 arm64 1:5.37-6ubuntu1 [71.0 kB] Get:25 http://ftpmaster.internal/ubuntu focal/main arm64 file arm64 1:5.37-6ubuntu1 [23.2 kB] Get:26 http://ftpmaster.internal/ubuntu focal/main arm64 libelf1 arm64 0.176-1.1build1 [44.2 kB] Get:27 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libglib2.0-0 arm64 2.63.3-3 [1191 kB] Get:28 http://ftpmaster.internal/ubuntu focal/main arm64 libicu63 arm64 63.2-2 [8146 kB] Get:29 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3.7-stdlib arm64 3.7.6-1ubuntu2 [1717 kB] Get:30 http://ftpmaster.internal/ubuntu focal/main arm64 libxml2 arm64 2.9.4+dfsg1-8ubuntu3 [575 kB] Get:31 http://ftpmaster.internal/ubuntu focal/main arm64 libyaml-0-2 arm64 0.2.2-1 [44.4 kB] Get:32 http://ftpmaster.internal/ubuntu focal/main arm64 python3-pkg-resources all 44.0.0-1 [100 kB] Get:33 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3-six all 1.14.0-2 [12.1 kB] Get:34 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3.7 arm64 3.7.6-1ubuntu2 [304 kB] Get:35 http://ftpmaster.internal/ubuntu focal/main arm64 ucf all 3.0038+nmu1 [51.6 kB] Get:36 http://ftpmaster.internal/ubuntu focal/main arm64 gettext-base arm64 0.19.8.1-10 [48.4 kB] Get:37 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5support0 arm64 1.17-6ubuntu3 [30.4 kB] Get:38 http://ftpmaster.internal/ubuntu focal/main arm64 libk5crypto3 arm64 1.17-6ubuntu3 [80.5 kB] Get:39 http://ftpmaster.internal/ubuntu focal/main arm64 libkeyutils1 arm64 1.6-6ubuntu1 [10.1 kB] Get:40 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5-3 arm64 1.17-6ubuntu3 [312 kB] Get:41 http://ftpmaster.internal/ubuntu focal/main arm64 libgssapi-krb5-2 arm64 1.17-6ubuntu3 [113 kB] Get:42 http://ftpmaster.internal/ubuntu focal/main arm64 libpsl5 arm64 0.20.2-2 [49.9 kB] Get:43 http://ftpmaster.internal/ubuntu focal/main arm64 libxau6 arm64 1:1.0.9-0ubuntu1 [7356 B] Get:44 http://ftpmaster.internal/ubuntu focal/main arm64 libxdmcp6 arm64 1:1.1.3-0ubuntu1 [10.3 kB] Get:45 http://ftpmaster.internal/ubuntu focal/main arm64 libxcb1 arm64 1.13.1-3build1 [43.8 kB] Get:46 http://ftpmaster.internal/ubuntu focal/main arm64 libx11-data all 2:1.6.8-1 [113 kB] Get:47 http://ftpmaster.internal/ubuntu focal/main arm64 libx11-6 arm64 2:1.6.8-1 [553 kB] Get:48 http://ftpmaster.internal/ubuntu focal/main arm64 libxext6 arm64 2:1.3.4-0ubuntu1 [27.7 kB] Get:49 http://ftpmaster.internal/ubuntu focal/main arm64 rubygems-integration all 1.15 [5056 B] Get:50 http://ftpmaster.internal/ubuntu focal/main arm64 rake all 12.3.3-1ubuntu1 [45.2 kB] Get:51 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-did-you-mean all 1.2.1-1 [9828 B] Get:52 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-minitest all 5.13.0-1 [40.9 kB] Get:53 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:54 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-power-assert all 1.1.1-1 [11.0 kB] Get:55 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-test-unit all 3.3.4-1 [73.1 kB] Get:56 http://ftpmaster.internal/ubuntu focal/main arm64 ruby-xmlrpc all 0.3.0-2 [23.8 kB] Get:57 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libruby2.5 arm64 2.5.7-1ubuntu3 [2948 kB] Get:58 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 ruby2.5 arm64 2.5.7-1ubuntu3 [48.6 kB] Get:59 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 ruby arm64 1:2.5.2ubuntu1 [5756 B] Get:60 http://ftpmaster.internal/ubuntu focal/universe arm64 ruby-asciidoctor all 2.0.10-2 [166 kB] Get:61 http://ftpmaster.internal/ubuntu focal/universe arm64 asciidoctor all 2.0.10-2 [40.3 kB] Get:62 http://ftpmaster.internal/ubuntu focal/main arm64 m4 arm64 1.4.18-4 [194 kB] Get:63 http://ftpmaster.internal/ubuntu focal/main arm64 autoconf all 2.69-11.1 [321 kB] Get:64 http://ftpmaster.internal/ubuntu focal/main arm64 autotools-dev all 20180224.1 [39.6 kB] Get:65 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 automake all 1:1.16.1-4ubuntu4 [522 kB] Get:66 http://ftpmaster.internal/ubuntu focal/main arm64 autopoint all 0.19.8.1-10 [412 kB] Get:67 http://ftpmaster.internal/ubuntu focal/main arm64 libtcl8.6 arm64 8.6.10+dfsg-1 [849 kB] Get:68 http://ftpmaster.internal/ubuntu focal/main arm64 libfreetype6 arm64 2.10.1-2 [316 kB] Get:69 http://ftpmaster.internal/ubuntu focal/universe arm64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:70 http://ftpmaster.internal/ubuntu focal/main arm64 fontconfig-config all 2.13.1-2ubuntu2 [28.9 kB] Get:71 http://ftpmaster.internal/ubuntu focal/main arm64 libfontconfig1 arm64 2.13.1-2ubuntu2 [111 kB] Get:72 http://ftpmaster.internal/ubuntu focal/main arm64 libxrender1 arm64 1:0.9.10-1 [16.1 kB] Get:73 http://ftpmaster.internal/ubuntu focal/main arm64 libxft2 arm64 2.3.3-0ubuntu1 [35.9 kB] Get:74 http://ftpmaster.internal/ubuntu focal/main arm64 x11-common all 1:7.7+19ubuntu13 [22.4 kB] Get:75 http://ftpmaster.internal/ubuntu focal/main arm64 libxss1 arm64 1:1.2.3-1 [8080 B] Get:76 http://ftpmaster.internal/ubuntu focal/main arm64 libtk8.6 arm64 8.6.10-1 [674 kB] Get:77 http://ftpmaster.internal/ubuntu focal/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-4 [478 kB] Get:78 http://ftpmaster.internal/ubuntu focal/main arm64 blt arm64 2.5.3+dfsg-4 [4944 B] Get:79 http://ftpmaster.internal/ubuntu focal/universe arm64 cd-hit arm64 4.8.1-2 [507 kB] Get:80 http://ftpmaster.internal/ubuntu focal/main arm64 libtool all 2.4.6-11 [194 kB] Get:81 http://ftpmaster.internal/ubuntu focal/main arm64 dh-autoreconf all 19 [16.1 kB] Get:82 http://ftpmaster.internal/ubuntu focal/main arm64 libdebhelper-perl all 12.7.3ubuntu1 [52.1 kB] Get:83 http://ftpmaster.internal/ubuntu focal/main arm64 libarchive-zip-perl all 1.67-1 [90.4 kB] Get:84 http://ftpmaster.internal/ubuntu focal/main arm64 libsub-override-perl all 0.09-2 [9532 B] Get:85 http://ftpmaster.internal/ubuntu focal/main arm64 libfile-stripnondeterminism-perl all 1.6.3-2 [16.0 kB] Get:86 http://ftpmaster.internal/ubuntu focal/main arm64 dh-strip-nondeterminism all 1.6.3-2 [5228 B] Get:87 http://ftpmaster.internal/ubuntu focal/main arm64 dwz arm64 0.13-5 [134 kB] Get:88 http://ftpmaster.internal/ubuntu focal/main arm64 libcroco3 arm64 0.6.13-1 [77.1 kB] Get:89 http://ftpmaster.internal/ubuntu focal/main arm64 gettext arm64 0.19.8.1-10 [851 kB] Get:90 http://ftpmaster.internal/ubuntu focal/main arm64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:91 http://ftpmaster.internal/ubuntu focal/main arm64 po-debconf all 1.0.21 [233 kB] Get:92 http://ftpmaster.internal/ubuntu focal/main arm64 debhelper all 12.7.3ubuntu1 [896 kB] Get:93 http://ftpmaster.internal/ubuntu focal/main arm64 python3-lib2to3 all 3.8.0-1 [75.6 kB] Get:94 http://ftpmaster.internal/ubuntu focal/main arm64 python3-distutils all 3.8.0-1 [142 kB] Get:95 http://ftpmaster.internal/ubuntu focal/main arm64 dh-python all 4.20191017ubuntu4 [88.2 kB] Get:96 http://ftpmaster.internal/ubuntu focal/main arm64 libbrotli1 arm64 1.0.7-6 [257 kB] Get:97 http://ftpmaster.internal/ubuntu focal/main arm64 libroken18-heimdal arm64 7.7.0+dfsg-1 [39.3 kB] Get:98 http://ftpmaster.internal/ubuntu focal/main arm64 libasn1-8-heimdal arm64 7.7.0+dfsg-1 [150 kB] Get:99 http://ftpmaster.internal/ubuntu focal/main arm64 libheimbase1-heimdal arm64 7.7.0+dfsg-1 [27.9 kB] Get:100 http://ftpmaster.internal/ubuntu focal/main arm64 libhcrypto4-heimdal arm64 7.7.0+dfsg-1 [86.5 kB] Get:101 http://ftpmaster.internal/ubuntu focal/main arm64 libwind0-heimdal arm64 7.7.0+dfsg-1 [47.2 kB] Get:102 http://ftpmaster.internal/ubuntu focal/main arm64 libhx509-5-heimdal arm64 7.7.0+dfsg-1 [98.6 kB] Get:103 http://ftpmaster.internal/ubuntu focal/main arm64 libkrb5-26-heimdal arm64 7.7.0+dfsg-1 [192 kB] Get:104 http://ftpmaster.internal/ubuntu focal/main arm64 libheimntlm0-heimdal arm64 7.7.0+dfsg-1 [14.8 kB] Get:105 http://ftpmaster.internal/ubuntu focal/main arm64 libgssapi3-heimdal arm64 7.7.0+dfsg-1 [88.3 kB] Get:106 http://ftpmaster.internal/ubuntu focal/main arm64 libsasl2-modules-db arm64 2.1.27+dfsg-2 [15.1 kB] Get:107 http://ftpmaster.internal/ubuntu focal/main arm64 libsasl2-2 arm64 2.1.27+dfsg-2 [48.4 kB] Get:108 http://ftpmaster.internal/ubuntu focal/main arm64 libldap-common all 2.4.48+dfsg-1ubuntu4 [16.9 kB] Get:109 http://ftpmaster.internal/ubuntu focal/main arm64 libldap-2.4-2 arm64 2.4.48+dfsg-1ubuntu4 [145 kB] Get:110 http://ftpmaster.internal/ubuntu focal/main arm64 libnghttp2-14 arm64 1.40.0-1 [75.2 kB] Get:111 http://ftpmaster.internal/ubuntu focal/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2build1 [53.3 kB] Get:112 http://ftpmaster.internal/ubuntu focal/main arm64 libssh-4 arm64 0.9.3-2ubuntu1 [159 kB] Get:113 http://ftpmaster.internal/ubuntu focal/main arm64 libcurl3-gnutls arm64 7.66.0-1ubuntu1 [211 kB] Get:114 http://ftpmaster.internal/ubuntu focal/universe arm64 libdeflate0 arm64 1.5-1 [80.3 kB] Get:115 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 libhts3 arm64 1.10.2-2 [325 kB] Get:116 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 samtools arm64 1.10-3 [474 kB] Get:117 http://ftpmaster.internal/ubuntu focal/universe arm64 fastaq all 3.17.0-2 [47.5 kB] Get:118 http://ftpmaster.internal/ubuntu focal/universe arm64 fonts-lyx all 2.3.3-3 [154 kB] Get:119 http://ftpmaster.internal/ubuntu focal/universe arm64 help2man arm64 1.47.12 [172 kB] Get:120 http://ftpmaster.internal/ubuntu focal/main arm64 libblas3 arm64 3.9.0-1 [89.1 kB] Get:121 http://ftpmaster.internal/ubuntu focal/main arm64 libcapnp-0.7.0 arm64 0.7.0-5 [930 kB] Get:122 http://ftpmaster.internal/ubuntu focal/main arm64 libexpat1-dev arm64 2.2.9-1 [103 kB] Get:123 http://ftpmaster.internal/ubuntu focal/universe arm64 libfml0 arm64 0.1-7 [64.8 kB] Get:124 http://ftpmaster.internal/ubuntu focal/main arm64 zlib1g-dev arm64 1:1.2.11.dfsg-1ubuntu3 [170 kB] Get:125 http://ftpmaster.internal/ubuntu focal/universe arm64 libfml-dev arm64 0.1-7 [77.9 kB] Get:126 http://ftpmaster.internal/ubuntu focal/main arm64 libgfortran5 arm64 9.2.1-25ubuntu1 [333 kB] Get:127 http://ftpmaster.internal/ubuntu focal/universe arm64 libgslcblas0 arm64 2.5+dfsg-6 [52.4 kB] Get:128 http://ftpmaster.internal/ubuntu focal/universe arm64 libgsl23 arm64 2.5+dfsg-6 [737 kB] Get:129 http://ftpmaster.internal/ubuntu focal/main arm64 libimagequant0 arm64 2.12.2-1.1 [29.3 kB] Get:130 http://ftpmaster.internal/ubuntu focal/main arm64 libjpeg-turbo8 arm64 2.0.3-0ubuntu1 [101 kB] Get:131 http://ftpmaster.internal/ubuntu focal/main arm64 libjpeg8 arm64 8c-2ubuntu8 [2198 B] Get:132 http://ftpmaster.internal/ubuntu focal/main arm64 libjs-jquery all 3.3.1~dfsg-3 [329 kB] Get:133 http://ftpmaster.internal/ubuntu focal/universe arm64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:134 http://ftpmaster.internal/ubuntu focal/main arm64 liblapack3 arm64 3.9.0-1 [1534 kB] Get:135 http://ftpmaster.internal/ubuntu focal/main arm64 liblcms2-2 arm64 2.9-4 [131 kB] Get:136 http://ftpmaster.internal/ubuntu focal/universe arm64 libminimap0 arm64 0.2-4 [20.9 kB] Get:137 http://ftpmaster.internal/ubuntu focal/universe arm64 libminimap-dev arm64 0.2-4 [32.1 kB] Get:138 http://ftpmaster.internal/ubuntu focal/universe arm64 libmurmurhash2 arm64 1.5-2 [6060 B] Get:139 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3.8 arm64 3.8.1-2ubuntu3 [1487 kB] Get:140 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3.8-dev arm64 3.8.1-2ubuntu3 [3740 kB] Get:141 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 libpython3-dev arm64 3.8.0-3 [7072 B] Get:142 http://ftpmaster.internal/ubuntu focal/main arm64 libjbig0 arm64 2.1-3.1build1 [24.0 kB] Get:143 http://ftpmaster.internal/ubuntu focal/main arm64 libwebp6 arm64 0.6.1-2 [155 kB] Get:144 http://ftpmaster.internal/ubuntu focal/main arm64 libtiff5 arm64 4.1.0+git191117-2 [150 kB] Get:145 http://ftpmaster.internal/ubuntu focal/main arm64 libwebpdemux2 arm64 0.6.1-2 [8868 B] Get:146 http://ftpmaster.internal/ubuntu focal/main arm64 libwebpmux3 arm64 0.6.1-2 [17.3 kB] Get:147 http://ftpmaster.internal/ubuntu focal/universe arm64 mash arm64 2.2.2+dfsg-1 [136 kB] Get:148 http://ftpmaster.internal/ubuntu focal/universe arm64 mummer arm64 3.23+dfsg-4 [790 kB] Get:149 http://ftpmaster.internal/ubuntu focal/universe arm64 python-matplotlib-data all 3.0.2-2ubuntu1 [3775 kB] Get:150 http://ftpmaster.internal/ubuntu focal/main arm64 python3-numpy arm64 1:1.17.4-5ubuntu2 [5447 kB] Get:151 http://ftpmaster.internal/ubuntu focal/main arm64 python3-reportlab-accel arm64 3.5.31-1 [23.3 kB] Get:152 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3-pil arm64 7.0.0-3 [371 kB] Get:153 http://ftpmaster.internal/ubuntu focal/main arm64 python3-reportlab all 3.5.31-1 [531 kB] Get:154 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-biopython arm64 1.76+dfsg-1 [1403 kB] Get:155 http://ftpmaster.internal/ubuntu focal/main arm64 python3-soupsieve all 1.9.5+dfsg-1 [29.1 kB] Get:156 http://ftpmaster.internal/ubuntu focal/main arm64 python3-bs4 all 4.8.2-1 [83.0 kB] Get:157 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-cycler all 0.10.0-2 [8024 B] Get:158 http://ftpmaster.internal/ubuntu focal/main arm64 python3-dateutil all 2.7.3-3ubuntu1 [63.3 kB] Get:159 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-dendropy all 4.4.0-2 [266 kB] Get:160 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3.8-dev arm64 3.8.1-2ubuntu3 [515 kB] Get:161 http://ftpmaster.internal/ubuntu focal-proposed/main arm64 python3-dev arm64 3.8.0-3 [1212 B] Get:162 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-kiwisolver arm64 1.0.1-2build3 [79.1 kB] Get:163 http://ftpmaster.internal/ubuntu focal/main arm64 python3-pyparsing all 2.4.2-1 [58.8 kB] Get:164 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-matplotlib arm64 3.0.2-2ubuntu1 [4537 kB] Get:165 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-nose all 1.3.7-4build1 [116 kB] Get:166 http://ftpmaster.internal/ubuntu focal/universe arm64 python3-pymummer all 0.10.3-2 [9312 B] Get:167 http://ftpmaster.internal/ubuntu focal-proposed/universe arm64 python3-pysam arm64 0.15.4+ds-1 [2342 kB] Get:168 http://ftpmaster.internal/ubuntu focal/main arm64 python3-setuptools all 44.0.0-1 [257 kB] Get:169 http://ftpmaster.internal/ubuntu focal/main arm64 python3-tk arm64 3.8.0-1 [110 kB] Get:170 http://ftpmaster.internal/ubuntu focal/universe arm64 bowtie2 arm64 2.3.5.1-6 [1295 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.6 MB in 3s (25.0 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 14657 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... Selecting previously unselected package libpython3.8-minimal:arm64. Preparing to unpack .../libpython3.8-minimal_3.8.1-2ubuntu3_arm64.deb ... Unpacking libpython3.8-minimal:arm64 (3.8.1-2ubuntu3) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.2.9-1_arm64.deb ... Unpacking libexpat1:arm64 (2.2.9-1) ... Selecting previously unselected package python3.8-minimal. Preparing to unpack .../python3.8-minimal_3.8.1-2ubuntu3_arm64.deb ... Unpacking python3.8-minimal (3.8.1-2ubuntu3) ... Setting up libpython3.8-minimal:arm64 (3.8.1-2ubuntu3) ... Setting up libexpat1:arm64 (2.2.9-1) ... Setting up python3.8-minimal (3.8.1-2ubuntu3) ... Selecting previously unselected package python3-minimal. (Reading database ... 14962 files and directories currently installed.) 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Setting up python3-minimal (3.8.0-3) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Selecting previously unselected package python3. (Reading database ... 15364 files and directories currently installed.) Preparing to unpack .../0-python3_3.8.0-3_arm64.deb ... Unpacking python3 (3.8.0-3) ... Selecting previously unselected package libpython3.7-minimal:arm64. Preparing to unpack .../1-libpython3.7-minimal_3.7.6-1ubuntu2_arm64.deb ... Unpacking libpython3.7-minimal:arm64 (3.7.6-1ubuntu2) ... Selecting previously unselected package python3.7-minimal. Preparing to unpack .../2-python3.7-minimal_3.7.6-1ubuntu2_arm64.deb ... Unpacking python3.7-minimal (3.7.6-1ubuntu2) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../3-libbsd0_0.10.0-1_arm64.deb ... Unpacking libbsd0:arm64 (0.10.0-1) ... 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Setting up liblcms2-2:arm64 (2.9-4) ... Setting up libxau6:arm64 (1:1.0.9-0ubuntu1) ... Setting up libkeyutils1:arm64 (1.6-6ubuntu1) ... Setting up libpsl5:arm64 (0.20.2-2) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up mime-support (3.64ubuntu1) ... Setting up libgslcblas0:arm64 (2.5+dfsg-6) ... Setting up libmurmurhash2:arm64 (1.5-2) ... Setting up ruby-power-assert (1.1.1-1) ... Setting up libmagic-mgc (1:5.37-6ubuntu1) ... Setting up gawk (1:5.0.1+dfsg-1) ... Setting up libarchive-zip-perl (1.67-1) ... Setting up libyaml-0-2:arm64 (0.2.2-1) ... Setting up libglib2.0-0:arm64 (2.63.3-3) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.3-3) ... Setting up libdebhelper-perl (12.7.3ubuntu1) ... Setting up libbrotli1:arm64 (1.0.7-6) ... Setting up x11-common (1:7.7+19ubuntu13) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:arm64 (1.40.0-1) ... Setting up libmagic1:arm64 (1:5.37-6ubuntu1) ... Setting up libdeflate0 (1.5-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up m4 (1.4.18-4) ... Setting up rubygems-integration (1.15) ... Setting up file (1:5.37-6ubuntu1) ... Setting up libldap-common (2.4.48+dfsg-1ubuntu4) ... Setting up libpython3.7-minimal:arm64 (3.7.6-1ubuntu2) ... Setting up libcapnp-0.7.0:arm64 (0.7.0-5) ... Setting up libfml0 (0.1-7) ... Setting up libjbig0:arm64 (2.1-3.1build1) ... Setting up libicu63:arm64 (63.2-2) ... Setting up libkrb5support0:arm64 (1.17-6ubuntu3) ... Setting up libsasl2-modules-db:arm64 (2.1.27+dfsg-2) ... Setting up ruby-minitest (5.13.0-1) ... Setting up libminimap0 (0.2-4) ... Setting up autotools-dev (20180224.1) ... Setting up libblas3:arm64 (3.9.0-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libexpat1-dev:arm64 (2.2.9-1) ... Setting up libfreetype6:arm64 (2.10.1-2) ... Setting up ruby-test-unit (3.3.4-1) ... Setting up libx11-data (2:1.6.8-1) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2build1) ... Setting up libgsl23:arm64 (2.5+dfsg-6) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libimagequant0:arm64 (2.12.2-1.1) ... Setting up mash (2.2.2+dfsg-1) ... Setting up libtcl8.6:arm64 (8.6.10+dfsg-1) ... Setting up autopoint (0.19.8.1-10) ... Setting up libwebp6:arm64 (0.6.1-2) ... Setting up ucf (3.0038+nmu1) ... Setting up libk5crypto3:arm64 (1.17-6ubuntu3) ... Setting up libjpeg-turbo8:arm64 (2.0.3-0ubuntu1) ... Setting up python3.7-minimal (3.7.6-1ubuntu2) ... Setting up libsasl2-2:arm64 (2.1.27+dfsg-2) ... Setting up libgfortran5:arm64 (9.2.1-25ubuntu1) ... Setting up libroken18-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up autoconf (2.69-11.1) ... Setting up zlib1g-dev:arm64 (1:1.2.11.dfsg-1ubuntu3) ... Setting up libuchardet0:arm64 (0.0.6-3) ... Setting up mummer (3.23+dfsg-4) ... Setting up libsub-override-perl (0.09-2) ... Setting up libkrb5-3:arm64 (1.17-6ubuntu3) ... Setting up libmpdec2:arm64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up libpython3.8-stdlib:arm64 (3.8.1-2ubuntu3) ... Setting up python3.8 (3.8.1-2ubuntu3) ... Setting up python-matplotlib-data (3.0.2-2ubuntu1) ... Setting up libwebpmux3:arm64 (0.6.1-2) ... Setting up libbsd0:arm64 (0.10.0-1) ... Setting up libelf1:arm64 (0.176-1.1build1) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libxml2:arm64 (2.9.4+dfsg1-8ubuntu3) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up libpython3-stdlib:arm64 (3.8.0-3) ... Setting up libheimbase1-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libjpeg8:arm64 (8c-2ubuntu8) ... Setting up automake (1:1.16.1-4ubuntu4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libxdmcp6:arm64 (1:1.1.3-0ubuntu1) ... Setting up libpython3.7-stdlib:arm64 (3.7.6-1ubuntu2) ... Setting up liblapack3:arm64 (3.9.0-1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.13.1-3build1) ... Setting up libfml-dev (0.1-7) ... Setting up libtool (2.4.6-11) ... Setting up fontconfig-config (2.13.1-2ubuntu2) ... Setting up libwebpdemux2:arm64 (0.6.1-2) ... Setting up libasn1-8-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up python3 (3.8.0-3) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libhcrypto4-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up bowtie2 (2.3.5.1-6) ... Setting up help2man (1.47.12) ... Setting up python3-six (1.14.0-2) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libwind0-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up python3-pyparsing (2.4.2-1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libpython3.8:arm64 (3.8.1-2ubuntu3) ... Setting up python3-cycler (0.10.0-2) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up python3-reportlab-accel:arm64 (3.5.31-1) ... Setting up bsdmainutils (11.1.2ubuntu2) ... 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:arm64 (1.17-6ubuntu3) ... Setting up libcroco3:arm64 (0.6.13-1) ... Setting up libminimap-dev (0.2-4) ... Setting up libssh-4:arm64 (0.9.3-2ubuntu1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up libx11-6:arm64 (2:1.6.8-1) ... Setting up python3-dateutil (2.7.3-3ubuntu1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libtiff5:arm64 (4.1.0+git191117-2) ... Setting up libfontconfig1:arm64 (2.13.1-2ubuntu2) ... Setting up python3-lib2to3 (3.8.0-1) ... Setting up python3-soupsieve (1.9.5+dfsg-1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up python3-pkg-resources (44.0.0-1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up python3-distutils (3.8.0-1) ... Setting up dh-python (4.20191017ubuntu4) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up python3.7 (3.7.6-1ubuntu2) ... Setting up gettext (0.19.8.1-10) ... Setting up python3-setuptools (44.0.0-1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libxrender1:arm64 (1:0.9.10-1) ... Setting up libhx509-5-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libxext6:arm64 (2:1.3.4-0ubuntu1) ... Setting up man-db (2.9.0-2) ... 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 (1.3.7-4build1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up python3-bs4 (4.8.2-1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-pil:arm64 (7.0.0-3) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libpython3.8-dev:arm64 (3.8.1-2ubuntu3) ... Setting up python3-kiwisolver (1.0.1-2build3) ... Setting up python3-numpy (1:1.17.4-5ubuntu2) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up python3.8-dev (3.8.1-2ubuntu3) ... Setting up python3-reportlab (3.5.31-1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up python3-biopython (1.76+dfsg-1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up python3-dendropy (4.4.0-2) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libkrb5-26-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up python3-matplotlib (3.0.2-2ubuntu1) ... /usr/lib/python3/dist-packages/matplotlib/backends/qt_editor/figureoptions.py:220: SyntaxWarning: "is not" with a literal. Did you mean "!="? if marker is not 'none': /usr/lib/python3/dist-packages/matplotlib/pyplot.py:2201: SyntaxWarning: "is" with a literal. Did you mean "=="? if fignum is False or fignum is 0: /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up libxft2:arm64 (2.3.3-0ubuntu1) ... Setting up libpython3-dev:arm64 (3.8.0-3) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:arm64 (8.6.10-1) ... Setting up libheimntlm0-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up libgssapi3-heimdal:arm64 (7.7.0+dfsg-1) ... Setting up python3-dev (3.8.0-3) ... 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:arm64 (2.4.48+dfsg-1ubuntu4) ... Setting up python3-tk:arm64 (3.8.0-1) ... Setting up libcurl3-gnutls:arm64 (7.66.0-1ubuntu1) ... Setting up libhts3:arm64 (1.10.2-2) ... Setting up python3-pysam (0.15.4+ds-1) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up samtools (1.10-3) ... Setting up fastaq (3.17.0-2) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up python3-pymummer (0.10.3-2) ... /usr/lib/python3.8/subprocess.py:838: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used self.stdin = io.open(p2cwrite, 'wb', bufsize) Setting up rake (12.3.3-1ubuntu1) ... Setting up libruby2.5:arm64 (2.5.7-1ubuntu3) ... Setting up dh-autoreconf (19) ... Setting up ruby2.5 (2.5.7-1ubuntu3) ... Setting up debhelper (12.7.3ubuntu1) ... Setting up ruby (1:2.5.2ubuntu1) ... Setting up ruby-asciidoctor (2.0.10-2) ... Setting up asciidoctor (2.0.10-2) ... Setting up sbuild-build-depends-ariba-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.30-0ubuntu3) ... Processing triggers for systemd (244.1-0ubuntu2) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-171-generic arm64 (aarch64) Toolchain package versions: binutils_2.33.90.20200122-1ubuntu2 dpkg-dev_1.19.7ubuntu2 g++-9_9.2.1-25ubuntu1 gcc-9_9.2.1-25ubuntu1 libc6-dev_2.30-0ubuntu3 libstdc++-9-dev_9.2.1-25ubuntu1 libstdc++6_9.2.1-25ubuntu1 linux-libc-dev_5.4.0-12.15 Package versions: adduser_3.118ubuntu1 advancecomp_2.1-2.1 apt_1.9.7 asciidoctor_2.0.10-2 autoconf_2.69-11.1 automake_1:1.16.1-4ubuntu4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11ubuntu2 base-passwd_3.5.47 bash_5.0-5ubuntu1 binutils_2.33.90.20200122-1ubuntu2 binutils-aarch64-linux-gnu_2.33.90.20200122-1ubuntu2 binutils-common_2.33.90.20200122-1ubuntu2 blt_2.5.3+dfsg-4 bowtie2_2.3.5.1-6 bsdmainutils_11.1.2ubuntu2 bsdutils_1:2.34-0.1ubuntu5 build-essential_12.8ubuntu1 bzip2_1.0.8-2 ca-certificates_20190110 cd-hit_4.8.1-2 coreutils_8.30-3ubuntu2 cpp_4:9.2.1-3.1ubuntu1 cpp-9_9.2.1-25ubuntu1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3ubuntu1 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20191017ubuntu4 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7ubuntu2 dpkg-dev_1.19.7ubuntu2 dwz_0.13-5 e2fsprogs_1.45.3-4ubuntu3 fakeroot_1.24-1 fastaq_3.17.0-2 fdisk_2.34-0.1ubuntu5 file_1:5.37-6ubuntu1 findutils_4.6.0+git+20190209-2ubuntu1 fontconfig-config_2.13.1-2ubuntu2 fonts-lyx_2.3.3-3 g++_4:9.2.1-3.1ubuntu1 g++-9_9.2.1-25ubuntu1 gawk_1:5.0.1+dfsg-1 gcc_4:9.2.1-3.1ubuntu1 gcc-9_9.2.1-25ubuntu1 gcc-9-base_9.2.1-25ubuntu1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpg_2.2.17-3ubuntu1 gpg-agent_2.2.17-3ubuntu1 gpgconf_2.2.17-3ubuntu1 gpgv_2.2.17-3ubuntu1 grep_3.3-1build1 groff-base_1.22.4-4 gzip_1.10-0ubuntu4 help2man_1.47.12 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-5ubuntu1 libapparmor1_2.13.3-7ubuntu1 libapt-pkg5.90_1.9.7 libarchive-zip-perl_1.67-1 libargon2-1_0~20171227-0.2 libasan5_9.2.1-25ubuntu1 libasn1-8-heimdal_7.7.0+dfsg-1 libassuan0_2.5.3-7ubuntu2 libatomic1_9.2.1-25ubuntu1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2ubuntu5 libaudit1_1:2.8.5-2ubuntu5 libbinutils_2.33.90.20200122-1ubuntu2 libblas3_3.9.0-1 libblkid1_2.34-0.1ubuntu5 libbrotli1_1.0.7-6 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-0ubuntu3 libc-dev-bin_2.30-0ubuntu3 libc6_2.30-0ubuntu3 libc6-dev_2.30-0ubuntu3 libcap-ng0_0.7.9-2.1build1 libcap2_1:2.27-1 libcapnp-0.7.0_0.7.0-5 libcc1-0_9.2.1-25ubuntu1 libcom-err2_1.45.3-4ubuntu3 libcroco3_0.6.13-1 libcryptsetup12_2:2.2.2-1ubuntu1 libctf-nobfd0_2.33.90.20200122-1ubuntu2 libctf0_2.33.90.20200122-1ubuntu2 libcurl3-gnutls_7.66.0-1ubuntu1 libdb5.3_5.3.28+dfsg1-0.6ubuntu1 libdebconfclient0_0.250ubuntu2 libdebhelper-perl_12.7.3ubuntu1 libdeflate0_1.5-1 libdevmapper1.02.1_2:1.02.155-2ubuntu7 libdpkg-perl_1.19.7ubuntu2 libelf1_0.176-1.1build1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.3-4ubuntu3 libfakeroot_1.24-1 libfdisk1_2.34-0.1ubuntu5 libffi6_3.2.1-9 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libfml-dev_0.1-7 libfml0_0.1-7 libfontconfig1_2.13.1-2ubuntu2 libfreetype6_2.10.1-2 libgcc-9-dev_9.2.1-25ubuntu1 libgcc1_1:9.2.1-25ubuntu1 libgcrypt20_1.8.5-3ubuntu1 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_9.2.1-25ubuntu1 libglib2.0-0_2.63.3-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2ubuntu2 libgomp1_9.2.1-25ubuntu1 libgpg-error0_1.36-7build1 libgsl23_2.5+dfsg-6 libgslcblas0_2.5+dfsg-6 libgssapi-krb5-2_1.17-6ubuntu3 libgssapi3-heimdal_7.7.0+dfsg-1 libhcrypto4-heimdal_7.7.0+dfsg-1 libheimbase1-heimdal_7.7.0+dfsg-1 libheimntlm0-heimdal_7.7.0+dfsg-1 libhogweed4_3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhts3_1.10.2-2 libhx509-5-heimdal_7.7.0+dfsg-1 libicu63_63.2-2 libidn2-0_2.2.0-2 libimagequant0_2.12.2-1.1 libip4tc2_1.8.3-2ubuntu5 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libpam-modules_1.3.1-5ubuntu4 libpam-modules-bin_1.3.1-5ubuntu4 libpam-runtime_1.3.1-5ubuntu4 libpam0g_1.3.1-5ubuntu4 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6build1 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpng16-16_1.6.37-1 libprocps7_2:3.3.15-2ubuntu3 libpsl5_0.20.2-2 libpython3-dev_3.8.0-3 libpython3-stdlib_3.8.0-3 libpython3.7-minimal_3.7.6-1ubuntu2 libpython3.7-stdlib_3.7.6-1ubuntu2 libpython3.8_3.8.1-2ubuntu3 libpython3.8-dev_3.8.1-2ubuntu3 libpython3.8-minimal_3.8.1-2ubuntu3 libpython3.8-stdlib_3.8.1-2ubuntu3 libreadline8_8.0-3 libroken18-heimdal_7.7.0+dfsg-1 librtmp1_2.4+20151223.gitfa8646d.1-2build1 libruby2.5_2.5.7-1ubuntu3 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2ubuntu2 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1ubuntu5 libsqlite3-0_3.30.1-1ubuntu1 libss2_1.45.3-4ubuntu3 libssh-4_0.9.3-2ubuntu1 libssl1.1_1.1.1d-2ubuntu3 libstdc++-9-dev_9.2.1-25ubuntu1 libstdc++6_9.2.1-25ubuntu1 libsub-override-perl_0.09-2 libsystemd0_244.1-0ubuntu2 libtasn1-6_4.15.0-2 libtcl8.6_8.6.10+dfsg-1 libtiff5_4.1.0+git191117-2 libtinfo6_6.1+20191019-1ubuntu1 libtk8.6_8.6.10-1 libtool_2.4.6-11 libtsan0_9.2.1-25ubuntu1 libubsan1_9.2.1-25ubuntu1 libuchardet0_0.0.6-3 libudev1_244.1-0ubuntu2 libunistring2_0.9.10-2 libuuid1_2.34-0.1ubuntu5 libwebp6_0.6.1-2 libwebpdemux2_0.6.1-2 libwebpmux3_0.6.1-2 libwind0-heimdal_7.7.0+dfsg-1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.9-0ubuntu1 libxcb1_1.13.1-3build1 libxdmcp6_1:1.1.3-0ubuntu1 libxext6_2:1.3.4-0ubuntu1 libxft2_2.3.3-0ubuntu1 libxml2_2.9.4+dfsg1-8ubuntu3 libxrender1_1:0.9.10-1 libxss1_1:1.2.3-1 libyaml-0-2_0.2.2-1 libzstd1_1.4.4+dfsg-1 linux-libc-dev_5.4.0-12.15 lockfile-progs_0.1.18 login_1:4.8-1ubuntu1 logsave_1.45.3-4ubuntu3 lsb-base_11.1.0ubuntu2 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mash_2.2.2+dfsg-1 mawk_1.3.3-17ubuntu3 mime-support_3.64ubuntu1 mount_2.34-0.1ubuntu5 mummer_3.23+dfsg-4 ncurses-base_6.1+20191019-1ubuntu1 ncurses-bin_6.1+20191019-1ubuntu1 openssl_1.1.1d-2ubuntu3 optipng_0.7.7-1 passwd_1:4.8-1ubuntu1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.28_5.28.1-6build1 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 pkgbinarymangler_144 po-debconf_1.0.21 policyrcd-script-zg2_0.1-3 procps_2:3.3.15-2ubuntu3 python-matplotlib-data_3.0.2-2ubuntu1 python3_3.8.0-3 python3-biopython_1.76+dfsg-1 python3-bs4_4.8.2-1 python3-cycler_0.10.0-2 python3-dateutil_2.7.3-3ubuntu1 python3-dendropy_4.4.0-2 python3-dev_3.8.0-3 python3-distutils_3.8.0-1 python3-kiwisolver_1.0.1-2build3 python3-lib2to3_3.8.0-1 python3-matplotlib_3.0.2-2ubuntu1 python3-minimal_3.8.0-3 python3-nose_1.3.7-4build1 python3-numpy_1:1.17.4-5ubuntu2 python3-pil_7.0.0-3 python3-pkg-resources_44.0.0-1 python3-pymummer_0.10.3-2 python3-pyparsing_2.4.2-1 python3-pysam_0.15.4+ds-1 python3-reportlab_3.5.31-1 python3-reportlab-accel_3.5.31-1 python3-setuptools_44.0.0-1 python3-six_1.14.0-2 python3-soupsieve_1.9.5+dfsg-1 python3-tk_3.8.0-1 python3.7_3.7.6-1ubuntu2 python3.7-minimal_3.7.6-1ubuntu2 python3.8_3.8.1-2ubuntu3 python3.8-dev_3.8.1-2ubuntu3 python3.8-minimal_3.8.1-2ubuntu3 rake_12.3.3-1ubuntu1 readline-common_8.0-3 ruby_1:2.5.2ubuntu1 ruby-asciidoctor_2.0.10-2 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.1-1 ruby-test-unit_3.3.4-1 ruby-xmlrpc_0.3.0-2 ruby2.5_2.5.7-1ubuntu3 rubygems-integration_1.15 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_244.1-0ubuntu2 systemd-sysv_244.1-0ubuntu2 sysvinit-utils_2.96-1ubuntu1 tar_1.30+dfsg-6 tk8.6-blt2.5_2.5.3+dfsg-4 ttf-bitstream-vera_1.10-8 tzdata_2019c-3 ubuntu-keyring_2018.09.18.1 ucf_3.0038+nmu1 util-linux_2.34-0.1ubuntu5 x11-common_1:7.7+19ubuntu13 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1ubuntu3 zlib1g-dev_1:1.2.11.dfsg-1ubuntu3 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Sat Jan 25 04:56:26 2020 UTC gpgv: using RSA key D56571B88A8BBAF140BF63D6BD7EAA60778FA6F5 gpgv: issuer "doko@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./ariba_2.14.4+ds-2build1.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-2build1.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-18608256 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-18608256 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-18608256 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-2build1 dpkg-buildpackage: info: source distribution focal dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/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-arm64' 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-arch dh build-arch --with python3 --buildsystem=pybuild dh_update_autotools_config -a -O--buildsystem=pybuild dh_autoreconf -a -O--buildsystem=pybuild dh_auto_configure -a -O--buildsystem=pybuild I: pybuild base:217: python3.8 setup.py config running config dh_auto_build -a -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/pubmlst_getter.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/report_flag_expander.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/scaffold_graph.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/mlst_reporter.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/ref_seq_chooser.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/report_filter.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 copying ariba/faidx.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/vfdb_parser.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/refdata_query.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/sequence_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/histogram.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/cluster.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/summary_cluster_variant.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/read_filter.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/flag.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/__init__.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/mic_plotter.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/read_store.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/samtools_variants.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/sequence_metadata.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/card_record.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/assembly_variants.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 creating /<>/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/prepareref.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/test.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/version.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/summary.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/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/__init__.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 copying ariba/tasks/expandflag.py -> /<>/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/prepareref_tb.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/clusters_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/mapping_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/ref_genes_getter_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/mlst_reporter_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/summary_cluster_variant_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/aln_to_metadata_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/cdhit_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/pubmlst_ref_preparer_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/sequence_variant_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/card_record_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/ref_preparer_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/read_filter_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/summary_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/histogram_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/assembly_variants_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/samtools_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/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/faidx_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/bam_parse_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/cluster_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/assembly_compare_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/ref_seq_chooser_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/pubmlst_getter_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/ref_seqs.fa -> /<>/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/reads_2.fq -> /<>/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_fasta_to_make_reads_from.fa -> /<>/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.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.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/panel.20181115.txt -> /<>/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 creating /<>/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/refcheck_test_fix_out.removed.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/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/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/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_keep_seqs_from_dict.log -> /<>/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_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/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/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/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/test_common_cat_files.out -> /<>/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/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/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/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/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/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/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_run_fermilite_fails.expected.log -> /<>/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/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/mapping_test_bowtie2_sorted.bam -> /<>/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/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/mlst_reporter.het_snp.out.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.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_2.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/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/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/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/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/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/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/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_sample_test_var_groups.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/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/reference_data_sequence_type.in.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/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/read_store_test_sort_file.out -> /<>/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/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/bam_parse_test_update_unmapped_mates_from_sam.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.out1.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/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_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/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/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/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/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/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/reference_data_load_rename_file.tsv -> /<>/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_load_user_clusters_file.bad3 -> /<>/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/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/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/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/report_filter_test_run.in.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/refcheck_test_check_duplicate_name.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/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/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/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/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/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/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/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_known_snp_presabs_nonc.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.2.tsv -> /<>/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/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/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/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/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/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/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/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/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_dummy_db.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/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/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_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/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/cluster_test_init_refdata.fa -> /<>/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/refcheck_test_check_too_long.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/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/refcheck_test_check_too_short.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/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/vfdb_parser_test_run.out.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/link_test_init.reads_2.fq -> /<>/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/assembly_run_fermilite_fail.reads.fq -> /<>/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/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/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/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_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/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/dummy.bam -> /<>/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/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/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_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/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/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/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_cat_genes_match_ref.fa -> /<>/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/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/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/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/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_make_reads_for_assembly.out2.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.allrefs.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.expect.depths.gz -> /<>/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/assembly_test_parse_assembly_bam.bam -> /<>/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/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/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/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/cluster_test_count_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.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/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/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_cdg.tsv -> /<>/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/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/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/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_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/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/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/reference_data_init_ok.params.json -> /<>/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/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/clusters_test_dummy_db.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/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/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/reference_data_load_metadata_tsv.tsv -> /<>/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_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/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/test_common_cat_files.in.1 -> /<>/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/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_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/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/vfdb_parser_test_run.in.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/refcheck_test_fix_in.fa -> /<>/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/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_variants_variants_only.fa -> /<>/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/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/refcheck_test_check_ok.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.exclude.tsv -> /<>/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_test_get_mummer_variants.snp.snps -> /<>/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/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/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/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/report_flag_expander.run.in.tsv -> /<>/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/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_all_metadata_tsvs.2.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.reads_1.fq -> /<>/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/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/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/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_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/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/link_test_init.reads_1.fq -> /<>/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/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/reference_data_write_metadata_tsv.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_2.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/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/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/mapping_test_bowtie2_unsorted.bam -> /<>/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/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/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/report_filter_test_run.expected.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/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/reference_data_init_ok.rename.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/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/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/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/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/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/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/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/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/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_clstrs_file.in.clstrs.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.allrefs.fa -> /<>/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/link_test_init.ref.fa.fai -> /<>/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/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/summary_test_load_fofn -> /<>/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/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/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/tb_genbank_to_gene_coords.gb -> /<>/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/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/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/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.3.fa -> /<>/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_write_metadata_tsv.expected.tsv -> /<>/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/mlst_profile_test.init.profile.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.fq -> /<>/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/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/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/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/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/refcheck_test_check_not_gene.fa -> /<>/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/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/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/clusters_test_dummy_reads_2.fq -> /<>/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/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/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/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/summary_to_matrix.1.tsv -> /<>/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/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/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/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_init_refdata.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/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/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/mapping_test_bowtie2_ref.fa -> /<>/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/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/bam_parse_test_parse.ref.fa -> /<>/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/read_store_test_sort_file.in -> /<>/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/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/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/mapping_test_bowtie2_reads_2.fq -> /<>/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/cdhit_test_fake_run.in.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.clusterrefs.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/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/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/assembly_run_fermilite.expected.log -> /<>/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/summary_test_write_distance_matrix.distances -> /<>/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/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/refdata_query_prepareref.in.tsv -> /<>/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/tb_write_prepareref_metadata_file.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/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/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/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_test_full_run_multiple_vars.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/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/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/refcheck_test_fix_out.rename -> /<>/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/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/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/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/refcheck_test_fix_out.log -> /<>/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/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/assembly_run_fermilite.expected.fa -> /<>/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/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/graph_test_update_from_sam.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_reads_2.fq -> /<>/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/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/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/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/mlst_reporter.profile.in.tsv -> /<>/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/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.yes.no_combinations.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/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/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_write_gene_fa.db.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.fa -> /<>/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/assembly_assemble_with_fermilite.expected.log -> /<>/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/read_store_test_get_reads.in -> /<>/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/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/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/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/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/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/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/clusters_test_load_minimap_files.cluster2representative -> /<>/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/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/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_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/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/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/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_load_vars_file_bad.1.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/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_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/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/mlst_profile_test.profile.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.in2.fq -> /<>/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/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/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/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/vfdb_parser_test_run.out.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.no.no_combinations.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.for_reads.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.reads.in.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.contigs.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/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/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/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/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_ok_presence_absence.metadata.tsv -> /<>/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/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_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/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/test_common_cat_files.in.3 -> /<>/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/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/pubmlst_rename_seqs.in.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/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/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_filter_bad_data.expected.log -> /<>/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_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/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/mapping_test_bowtie2_ref.fa.fai -> /<>/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/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/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/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/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/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/summary_test_whole_run.out.csv -> /<>/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/link_test_init.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_nonc.tsv -> /<>/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/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/refcheck_test_fix_out.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/report_filter_test_init_good.tsv -> /<>/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/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/mapping_test_sam_to_fastq.bam -> /<>/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/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/cluster_test_count_reads_1.fq -> /<>/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/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/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/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/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_ok_gene_start_mismatch.fa -> /<>/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/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/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/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/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/refdata_query_prepareref.in.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/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/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/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/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/clusters_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.hist -> /<>/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/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_init_fails.empty.tsv -> /<>/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/mlst_reporter.het_snps.out.tsv -> /<>/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/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/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/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/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/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/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/reference_data_init_fails.in.fa -> /<>/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/clusters_test_load_data_info_file -> /<>/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/cdhit_test_load_user_clusters_file.good -> /<>/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/00.rename_info -> /<>/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/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/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.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/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/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.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/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/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/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/01.filter.check_metadata.log -> /<>/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_2.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_1.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_2.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_1.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_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 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 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.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/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/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.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/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/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.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/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/01.filter.check_noncoding.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/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/01.filter.check_metadata.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/00.rename_info -> /<>/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/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/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.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/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/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.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/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/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/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/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 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.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/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/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.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/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/01.filter.check_metadata.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.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.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.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/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/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/01.filter.check_metadata.log -> /<>/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_2.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_1.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_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/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/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_2.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_1.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_2.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_1.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_2.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_1.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_2.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_1.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_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/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/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_2.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_1.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_2.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_1.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_2.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_1.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_2.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_1.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_2.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_1.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.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/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/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.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/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/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.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/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/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 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/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 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_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 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 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_2.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_1.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_2.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_1.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_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 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 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/reads_1.fq -> /<>/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 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/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/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/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 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 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_2.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_1.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_2.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_1.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_2.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_1.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_2.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_1.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_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/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/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/reads_2.fq -> /<>/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 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_2.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_1.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-arm64-3.8 creating build/temp.linux-arm64-3.8/ariba creating build/temp.linux-arm64-3.8/ariba/ext aarch64-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-arm64-3.8/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); | ~~~~~~^~~~~~~~~~~~~~ aarch64-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-arm64-3.8/ariba/ext/minimap_ariba.o -o /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/minimap_ariba.cpython-38-aarch64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -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-arm64-3.8/ariba/ext/fml-asm_ariba.o aarch64-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-arm64-3.8/ariba/ext/fml-asm_ariba.o -o /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/fermilite_ariba.cpython-38-aarch64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension aarch64-linux-gnu-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -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-arm64-3.8/ariba/ext/vcfcall_ariba.o aarch64-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-arm64-3.8/ariba/ext/vcfcall_ariba.o -o /<>/ariba-2.14.4+ds/.pybuild/cpython3_3.8_ariba/build/vcfcall_ariba.cpython-38-aarch64-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 664 to 775 dh_auto_test -a -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 215.908s OK (SKIP=2) create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary-arch dh binary-arch --with python3 --buildsystem=pybuild dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install -a -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-aarch64-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/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/cdhit.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/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/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/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/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/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/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/pubmlstspecies.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__/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__/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__/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__/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__/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/__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__/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__/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__/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__/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__/__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__/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__/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__/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__/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/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/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/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/__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/reportfilter.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/pubmlstget.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/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_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/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/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/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/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/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/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/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/report.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/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/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/external_progs.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/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/aln_to_metadata.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/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.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.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/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/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/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/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/histogram.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/cluster.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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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/__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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/__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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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/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/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/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/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/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/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/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/__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/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/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/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/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/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/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/versions.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/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/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/reads_2.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/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_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/sequence_metadata.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/ncbi_getter_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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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/__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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/__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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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__/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/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/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/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/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/summary_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/histogram_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/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/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/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/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/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/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_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/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_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/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/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/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/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/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/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/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/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/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/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/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_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/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/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/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/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/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/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/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/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/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/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/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/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/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 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/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/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_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/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/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/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/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/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/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/samtools_variants_test_get_variants.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/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/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 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_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/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_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/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/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_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/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/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/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/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/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/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/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_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/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/assembly_variants_test_get_variants_presence_absence.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_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_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/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_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/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/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/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/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/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/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/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/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/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/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/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/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_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/summary_gather_unfiltered_output_data.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_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/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/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/graph_test_update_from_sam.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/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/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/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.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/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/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.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/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/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_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/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/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/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/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/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/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_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/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/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/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_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/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/cluster_test_init_refdata.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.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_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/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/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/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/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/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/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/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/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/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/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/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/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/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/pubmlst_rename_seqs.expected.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_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_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 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_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/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/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/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/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/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 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.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/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/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.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/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/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/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.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.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/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/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/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/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/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/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/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_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/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/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/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/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/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_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/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/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_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/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/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/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/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/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/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/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/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/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/faidx_test_write_fa_subset.in.fa.fai -> /<>/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/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/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/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/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.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/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/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.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/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/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/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/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/assembly_variants_one_var_one_ctg_cdg.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_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_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/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/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 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_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/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/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/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/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/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_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/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 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/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/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/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/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/bam_parse_test_parse.reads_2.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_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_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/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/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/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/reference_data_load_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/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_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/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/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/assembly_test_check_spades_log_file.log.bad -> /<>/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_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/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/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/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_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/cluster_test_full_run_assembly_fail.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/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/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/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/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/assembly_test_scaffold_with_sspace_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_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_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_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_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/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/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/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/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/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/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/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/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/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/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/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/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/summary_sample_test_column_summary_data.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.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/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/summary_to_matrix.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_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_variants_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/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/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/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/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/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_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/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/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/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/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 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/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/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_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/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/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/aln_to_metadata_run_coding.out.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/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/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/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/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/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/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_all_non_wild_type_variants.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_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/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/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/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/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/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/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/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/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/mapping_test_bowtie2_unsorted.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/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 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/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/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/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/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/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/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/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/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/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/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/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/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 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.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/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/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.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/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/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.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/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/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/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/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 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/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/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 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_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/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/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/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/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_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/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 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_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/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/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/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/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/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/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/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/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/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/tb_genbank_to_gene_coords.gb -> /<>/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_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/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/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/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/read_filter_test_run.expected.reads_2.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_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_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/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/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.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/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_write_metadata_tsv.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/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/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/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/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/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/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/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/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/refcheck_test_check_not_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_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_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 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/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/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/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/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/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/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/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/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/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/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/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/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/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_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_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/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/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 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_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/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/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/mapping_test_bowtie2_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/summary_test_write_distance_matrix.distances -> /<>/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_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/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_ok_non_coding.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/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/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/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/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/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/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 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_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/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/summary_sample_test_non_synon_variants.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_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/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_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/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/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/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/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/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/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 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/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/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/refcheck_test_fix_out.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_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/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 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_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/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/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/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/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/graph_test_update_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/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/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/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/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/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/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/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/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.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/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/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/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_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/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 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 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/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/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/reference_data_remove_bad_noncoding.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_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_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/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/best_seq_chooser_best_seq_ref.fa.fai -> /<>/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 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_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/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/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/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/samtools_variants_test_get_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_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_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/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 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/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/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/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/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.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/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/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.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/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/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/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/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/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/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/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/aln_to_metadata_make_cluster_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/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/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/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/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/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/clusters_test_load_minimap_files.cluster2representative -> /<>/ariba-2.14.4+ds/debian/ariba/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/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/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_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/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/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/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_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/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/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_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/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/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/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/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/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/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/cluster_full_run_smtls_snp_varonly_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/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/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/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 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/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/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/mlst_reporter.new_st.report.in.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_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/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/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/ref_preparer_test_run.in.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/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_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/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/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_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/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/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/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/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/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/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/mapping_test_get_total_alignment_score.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_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_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/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/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_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/mic_plotter_load_mic_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 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/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/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_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_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/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 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/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 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/refdata_query_prepareref.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/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 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_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 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/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/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/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/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/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/clusters_minimap_reads_to_all_refs.out.hist -> /<>/ariba-2.14.4+ds/debian/ariba/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/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_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/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/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/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/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 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_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/__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/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/faidx_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/minimap_ariba.cpython-38-aarch64-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/fermilite_ariba.cpython-38-aarch64-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/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/cdhit.py to cdhit.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/prepareref.py to prepareref.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/test.py to test.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/version.py to version.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/summary.py to summary.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/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/__init__.py to __init__.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/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/pubmlstget.py to pubmlstget.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/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_compare.py to assembly_compare.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/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/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/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/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/tb.py to tb.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/report.py to report.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/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/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/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/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/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/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/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/histogram.py to histogram.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/cluster.py to cluster.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/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/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/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/summary.py to summary.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/common.py to common.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/link.py to link.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/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/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/clusters.py to clusters.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/versions.py to versions.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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/__init__.py to __init__.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/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/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/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/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/cluster_test.py to cluster_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/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/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/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/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/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/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/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/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/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/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 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 775 dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -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 -a -O--buildsystem=pybuild dh_installinit -a -O--buildsystem=pybuild dh_installsystemduser -a -O--buildsystem=pybuild dh_perl -a -O--buildsystem=pybuild dh_link -a -O--buildsystem=pybuild dh_strip_nondeterminism -a -O--buildsystem=pybuild dh_compress -a -O--buildsystem=pybuild dh_fixperms -a -O--buildsystem=pybuild dh_missing -a -O--buildsystem=pybuild dh_dwz -a -O--buildsystem=pybuild dh_strip -a -O--buildsystem=pybuild dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/ariba/usr/lib/python3/dist-packages/vcfcall_ariba.cpython-38-aarch64-linux-gnu.so was not linked against libpthread.so.0 (it uses none of the library's symbols) dh_installdeb -a -O--buildsystem=pybuild dh_gencontrol -a -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 -a -O--buildsystem=pybuild dh_builddeb -a -O--buildsystem=pybuild INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing ariba (in debian/ariba); do_strip: , oemstrip: pkgstriptranslations: processing ariba-dbgsym (in debian/.debhelper/ariba/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/ariba/DEBIAN/control, package ariba, directory debian/ariba 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-2build1_arm64.deb'. 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-2build1_arm64.deb'. Renaming ariba-dbgsym_2.14.4+ds-2build1_arm64.deb to ariba-dbgsym_2.14.4+ds-2build1_arm64.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../ariba_2.14.4+ds-2build1_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 20200125-0505 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ ariba_2.14.4+ds-2build1_arm64.changes: -------------------------------------- Format: 1.8 Date: Sat, 25 Jan 2020 04:30:04 +0000 Source: ariba Binary: ariba Architecture: arm64 Version: 2.14.4+ds-2build1 Distribution: focal-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Matthias Klose Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.14.4+ds-2build1) focal; urgency=medium . * No-change rebuild to build with python3.8. Checksums-Sha1: 5e05cd7c686862d5569d84a533c1529186f339e3 389416 ariba-dbgsym_2.14.4+ds-2build1_arm64.ddeb b5c160d148c9770d779dfe16dac8b54b91a1c4af 9877 ariba_2.14.4+ds-2build1_arm64.buildinfo fb081ef26a5bcb7d6a7c33083125c597a9b99c09 1939724 ariba_2.14.4+ds-2build1_arm64.deb Checksums-Sha256: 17f340821ffde4ef2da6f122971f84697e9e7e1176e53b089081cf04e037fbe6 389416 ariba-dbgsym_2.14.4+ds-2build1_arm64.ddeb e04ca5605c1dd10eea1455b5d85bee60626ae10288fd7f435ba46855ed9de548 9877 ariba_2.14.4+ds-2build1_arm64.buildinfo f7e83d27a0e217ae3bdee72acb6b4b997c86f97f3e2f2a41d330be495a8ad7b9 1939724 ariba_2.14.4+ds-2build1_arm64.deb Files: 393e727bcd8477d36677b2dc3219d139 389416 debug optional ariba-dbgsym_2.14.4+ds-2build1_arm64.ddeb 1c67937d481477930f323597151c861c 9877 science optional ariba_2.14.4+ds-2build1_arm64.buildinfo 2a1f45001ca77576a8c0d20c9a44aa55 1939724 science optional ariba_2.14.4+ds-2build1_arm64.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ ariba_2.14.4+ds-2build1_arm64.deb --------------------------------- new debian package, version 2.0. size 1939724 bytes: control archive=17864 bytes. 1123 bytes, 17 lines control 91137 bytes, 756 lines md5sums 236 bytes, 12 lines * postinst #!/bin/sh 385 bytes, 12 lines * prerm #!/bin/sh Package: ariba Version: 2.14.4+ds-2build1 Architecture: arm64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 20430 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 (>= 2.17), libfml0 (>= 0.1-4~), libgcc1 (>= 1:3.0), libminimap0, 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 2020-01-25 04:30 ./ drwxr-xr-x root/root 0 2020-01-25 04:30 ./usr/ drwxr-xr-x root/root 0 2020-01-25 04:30 ./usr/bin/ -rwxr-xr-x root/root 26193 2020-01-25 04:30 ./usr/bin/ariba drwxr-xr-x root/root 0 2020-01-25 04:30 ./usr/lib/ drwxr-xr-x root/root 0 2020-01-25 04:30 ./usr/lib/python3/ drwxr-xr-x root/root 0 2020-01-25 04:30 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2020-01-25 04:30 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/ -rw-r--r-- root/root 519 2020-01-25 04:30 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/PKG-INFO -rw-r--r-- root/root 1 2020-01-25 04:30 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2020-01-25 04:30 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/requires.txt -rw-r--r-- root/root 50 2020-01-25 04:30 ./usr/lib/python3/dist-packages/ariba-2.14.4.egg-info/top_level.txt drwxr-xr-x root/root 0 2020-01-25 04:30 ./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 14:23 ./usr/lib/python3/dist-packages/ariba/cluster.py -rw-r--r-- root/root 28393 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/clusters.py -rw-r--r-- root/root 2380 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/common.py -rw-r--r-- root/root 5279 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/external_progs.py -rw-r--r-- root/root 324 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/faidx.py -rw-r--r-- root/root 1430 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/flag.py -rw-r--r-- root/root 1339 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/histogram.py -rw-r--r-- root/root 3981 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/link.py -rw-r--r-- root/root 5037 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/mapping.py -rw-r--r-- root/root 2078 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/megares_data_finder.py -rw-r--r-- root/root 4577 2019-09-24 14:23 ./usr/lib/python3/dist-packages/ariba/megares_zip_parser.py 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Build-Time: 276 Distribution: focal-proposed Host Architecture: arm64 Install-Time: 73 Job: ariba_2.14.4+ds-2build1.dsc Machine Architecture: arm64 Package: ariba Package-Time: 351 Source-Version: 2.14.4+ds-2build1 Space: 77208 Status: successful Version: 2.14.4+ds-2build1 -------------------------------------------------------------------------------- Finished at 20200125-0505 Build needed 00:05:51, 77208k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=focal --arch=arm64 PACKAGEBUILD-18608256 Scanning for processes to kill in build PACKAGEBUILD-18608256