https://launchpad.net/ubuntu/+source/ariba/2.14.6+ds-3build1/+build/23248863 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux riscv64-qemu-lcy01-007 5.11.0-1029-generic #32~20.04.1-Ubuntu SMP Fri Jan 28 13:38:22 UTC 2022 riscv64 Buildd toolchain package versions: launchpad-buildd_209~536~ubuntu20.04.1 python3-lpbuildd_209~536~ubuntu20.04.1 sbuild_0.79.0-1ubuntu1 git_1:2.25.1-1ubuntu3.2 dpkg-dev_1.19.7ubuntu3 python3-debian_0.1.36ubuntu1. Syncing the system clock with the buildd NTP service... 17 Mar 17:12:06 ntpdate[3605439]: adjust time server 10.211.37.1 offset -0.000321 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23248863 --image-type chroot /home/buildd/filecache-default/03bec7884d85d5bd8bcd177f093129b6620b2195 Creating target for build PACKAGEBUILD-23248863 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23248863 Starting target for build PACKAGEBUILD-23248863 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23248863 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-23248863 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23248863 Updating target for build PACKAGEBUILD-23248863 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main riscv64 Packages [1298 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [514 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe riscv64 Packages [12.9 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5644 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 Packages [71.6 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [34.3 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe riscv64 Packages [350 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [187 kB] Fetched 21.6 MB in 36s (599 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: libperl5.32 libssl1.1 perl-modules-5.32 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: gcc-12-base libperl5.34 libsemanage2 libsepol2 libssl3 perl-modules-5.34 The following packages will be upgraded: apt base-files bash binutils binutils-common binutils-riscv64-linux-gnu bsdutils bzip2 ca-certificates coreutils cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs fakeroot g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep init init-system-helpers libacl1 libapparmor1 libapt-pkg6.0 libargon2-1 libasan6 libatomic1 libattr1 libaudit-common libaudit1 libbinutils libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl libext2fs2 libfakeroot libffi8 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libprocps8 libreadline8 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libudev1 libunistring2 libuuid1 libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base pkgbinarymangler procps readline-common sed sensible-utils systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata usrmerge util-linux zlib1g 131 upgraded, 6 newly installed, 1 to remove and 0 not upgraded. Need to get 89.8 MB of archives. After this operation, 53.9 MB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcrypt-dev riscv64 1:4.4.27-1 [249 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main riscv64 libc6-dev riscv64 2.35-0ubuntu3 [3236 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main riscv64 libc-dev-bin riscv64 2.35-0ubuntu3 [18.9 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main riscv64 libaudit-common all 1:3.0.7-1 [4782 B] Get:5 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcap-ng0 riscv64 0.7.9-2.2build3 [10.3 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main riscv64 libaudit1 riscv64 1:3.0.7-1 [45.5 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main riscv64 perl-modules-5.34 all 5.34.0-3ubuntu1 [2975 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main riscv64 libperl5.34 riscv64 5.34.0-3ubuntu1 [4206 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main riscv64 perl riscv64 5.34.0-3ubuntu1 [232 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main riscv64 perl-base riscv64 5.34.0-3ubuntu1 [1639 kB] Get:11 http://ftpmaster.internal/ubuntu jammy/main riscv64 bzip2 riscv64 1.0.8-5 [33.9 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main riscv64 libbz2-1.0 riscv64 1.0.8-5 [36.2 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgdbm6 riscv64 1.23-1 [29.9 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgdbm-compat4 riscv64 1.23-1 [5860 B] Get:15 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 zlib1g riscv64 1:1.2.11.dfsg-2ubuntu8 [55.8 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main riscv64 debconf all 1.5.79ubuntu1 [126 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpam0g riscv64 1.4.0-11ubuntu1 [56.4 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcrypt1 riscv64 1:4.4.27-1 [97.4 kB] Get:19 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 linux-libc-dev riscv64 5.15.0-23.23 [1280 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main riscv64 libc6 riscv64 2.35-0ubuntu3 [2640 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main riscv64 libc-bin riscv64 2.35-0ubuntu3 [561 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main riscv64 gcc-12-base riscv64 12-20220313-1ubuntu1 [18.9 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgcc-s1 riscv64 12-20220313-1ubuntu1 [44.1 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main riscv64 base-files riscv64 12ubuntu2 [62.9 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main riscv64 debianutils riscv64 5.5-1ubuntu1 [105 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main riscv64 bash riscv64 5.1-6ubuntu1 [647 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main riscv64 bsdutils riscv64 1:2.37.2-4ubuntu3 [91.4 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main riscv64 coreutils riscv64 8.32-4.1ubuntu1 [1318 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgpg-error0 riscv64 1.43-3 [63.8 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgcrypt20 riscv64 1.9.4-3ubuntu2 [498 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main riscv64 libstdc++6 riscv64 12-20220313-1ubuntu1 [690 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main riscv64 libssl3 riscv64 3.0.1-0ubuntu1 [1449 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main riscv64 libargon2-1 riscv64 0~20171227-0.3 [19.7 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main riscv64 libblkid1 riscv64 2.37.2-4ubuntu3 [149 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpcre2-8-0 riscv64 10.39-3 [136 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main riscv64 libselinux1 riscv64 3.3-1build1 [71.0 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main riscv64 libudev1 riscv64 249.11-0ubuntu1 [70.3 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main riscv64 libdevmapper1.02.1 riscv64 2:1.02.175-2.1ubuntu4 [131 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main riscv64 libuuid1 riscv64 2.37.2-4ubuntu3 [27.3 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcryptsetup12 riscv64 2:2.4.3-1ubuntu1 [184 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgmp10 riscv64 2:6.2.1+dfsg-3ubuntu1 [245 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main riscv64 libunistring2 riscv64 1.0-1 [540 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main riscv64 libidn2-0 riscv64 2.3.2-2 [67.5 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main riscv64 libffi8 riscv64 3.4.2-4 [20.4 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main riscv64 libp11-kit0 riscv64 0.24.0-6 [203 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main riscv64 libtasn1-6 riscv64 4.18.0-4 [38.9 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgnutls30 riscv64 3.7.3-4ubuntu1 [870 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main riscv64 systemd-sysv riscv64 249.11-0ubuntu1 [10.5 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main riscv64 systemd-timesyncd riscv64 249.11-0ubuntu1 [28.9 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main riscv64 libacl1 riscv64 2.3.1-1 [15.3 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main riscv64 libapparmor1 riscv64 3.0.4-2ubuntu2 [34.2 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main riscv64 libip4tc2 riscv64 1.8.7-1ubuntu4 [18.1 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main riscv64 libzstd1 riscv64 1.4.8+dfsg-3 [370 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main riscv64 libkmod2 riscv64 29-1ubuntu1 [42.1 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main riscv64 libmount1 riscv64 2.37.2-4ubuntu3 [157 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main riscv64 libseccomp2 riscv64 2.5.3-2ubuntu1 [45.1 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main riscv64 login riscv64 1:4.8.1-2ubuntu2 [184 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main riscv64 util-linux riscv64 2.37.2-4ubuntu3 [1124 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main riscv64 mount riscv64 2.37.2-4ubuntu3 [129 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main riscv64 systemd riscv64 249.11-0ubuntu1 [4145 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsystemd0 riscv64 249.11-0ubuntu1 [292 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxxhash0 riscv64 0.8.1-1 [31.9 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main riscv64 libapt-pkg6.0 riscv64 2.4.1 [916 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main riscv64 dpkg riscv64 1.21.1ubuntu1 [1214 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main riscv64 dash riscv64 0.5.11+git20210903+057cd650a4ed-3 [86.3 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main riscv64 grep riscv64 3.7-1 [151 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main riscv64 libncurses6 riscv64 6.3-2 [93.6 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main riscv64 libncursesw6 riscv64 6.3-2 [128 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main riscv64 libtinfo6 riscv64 6.3-2 [96.1 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main riscv64 ncurses-bin riscv64 6.3-2 [176 kB] Get:71 http://ftpmaster.internal/ubuntu jammy/main riscv64 sed riscv64 4.8-1ubuntu1 [187 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main riscv64 init-system-helpers all 1.62 [38.5 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main riscv64 ncurses-base all 6.3-2 [20.1 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main riscv64 sysvinit-utils riscv64 3.01-1ubuntu1 [20.8 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main riscv64 gpgv riscv64 2.2.27-3ubuntu1 [195 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main riscv64 apt riscv64 2.4.1 [1338 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsepol2 riscv64 3.3-1 [254 kB] Get:78 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libsemanage-common all 3.3-1build2 [9874 B] Get:79 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libsemanage2 riscv64 3.3-1build2 [83.9 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main riscv64 passwd riscv64 1:4.8.1-2ubuntu2 [736 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpam-modules-bin riscv64 1.4.0-11ubuntu1 [36.9 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpam-modules riscv64 1.4.0-11ubuntu1 [265 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main riscv64 logsave riscv64 1.46.5-2ubuntu1 [10.1 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main riscv64 libext2fs2 riscv64 1.46.5-2ubuntu1 [196 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/main riscv64 e2fsprogs riscv64 1.46.5-2ubuntu1 [554 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main riscv64 init riscv64 1.62 [5414 B] Get:87 http://ftpmaster.internal/ubuntu jammy/main riscv64 libattr1 riscv64 1:2.5.1-1 [12.7 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcom-err2 riscv64 1.46.5-2ubuntu1 [8838 B] Get:89 http://ftpmaster.internal/ubuntu jammy/main riscv64 libdebconfclient0 riscv64 0.261ubuntu1 [6560 B] Get:90 http://ftpmaster.internal/ubuntu jammy/main riscv64 libk5crypto3 riscv64 1.19.2-2 [102 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main riscv64 libkrb5support0 riscv64 1.19.2-2 [30.7 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main riscv64 libkrb5-3 riscv64 1.19.2-2 [337 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgssapi-krb5-2 riscv64 1.19.2-2 [127 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main riscv64 libkeyutils1 riscv64 1.6.1-2ubuntu3 [9204 B] Get:95 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpam-runtime all 1.4.0-11ubuntu1 [40.2 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsmartcols1 riscv64 2.37.2-4ubuntu3 [103 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgomp1 riscv64 12-20220313-1ubuntu1 [111 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main riscv64 libatomic1 riscv64 12-20220313-1ubuntu1 [7864 B] Get:99 http://ftpmaster.internal/ubuntu jammy/main riscv64 libasan6 riscv64 11.2.0-18ubuntu1 [2106 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/main riscv64 g++-11 riscv64 11.2.0-18ubuntu1 [9289 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/main riscv64 gcc-11 riscv64 11.2.0-18ubuntu1 [15.9 MB] Get:102 http://ftpmaster.internal/ubuntu jammy/main riscv64 libstdc++-11-dev riscv64 11.2.0-18ubuntu1 [4757 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgcc-11-dev riscv64 11.2.0-18ubuntu1 [2392 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/main riscv64 libisl23 riscv64 0.24-2 [593 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/main riscv64 libmpc3 riscv64 1.2.1-1 [44.4 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcc1-0 riscv64 12-20220313-1ubuntu1 [43.6 kB] Get:107 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libctf0 riscv64 2.38-3ubuntu1 [97.9 kB] Get:108 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libctf-nobfd0 riscv64 2.38-3ubuntu1 [99.7 kB] Get:109 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 binutils-riscv64-linux-gnu riscv64 2.38-3ubuntu1 [927 kB] Get:110 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libbinutils riscv64 2.38-3ubuntu1 [492 kB] Get:111 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 binutils riscv64 2.38-3ubuntu1 [3096 B] Get:112 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 binutils-common riscv64 2.38-3ubuntu1 [213 kB] Get:113 http://ftpmaster.internal/ubuntu jammy/main riscv64 cpp-11 riscv64 11.2.0-18ubuntu1 [7984 kB] Get:114 http://ftpmaster.internal/ubuntu jammy/main riscv64 gcc-11-base riscv64 11.2.0-18ubuntu1 [21.1 kB] Get:115 http://ftpmaster.internal/ubuntu jammy/main riscv64 libprocps8 riscv64 2:3.3.17-6ubuntu2 [32.7 kB] Get:116 http://ftpmaster.internal/ubuntu jammy/main riscv64 libss2 riscv64 1.46.5-2ubuntu1 [10.7 kB] Get:117 http://ftpmaster.internal/ubuntu jammy/main riscv64 mawk riscv64 1.3.4.20200120-3 [95.0 kB] Get:118 http://ftpmaster.internal/ubuntu jammy/main riscv64 procps riscv64 2:3.3.17-6ubuntu2 [372 kB] Get:119 http://ftpmaster.internal/ubuntu jammy/main riscv64 sensible-utils all 0.0.17 [20.1 kB] Get:120 http://ftpmaster.internal/ubuntu jammy/main riscv64 usrmerge all 25ubuntu2 [54.7 kB] Get:121 http://ftpmaster.internal/ubuntu jammy/main riscv64 openssl riscv64 3.0.1-0ubuntu1 [1141 kB] Get:122 http://ftpmaster.internal/ubuntu jammy/main riscv64 ca-certificates all 20211016 [148 kB] Get:123 http://ftpmaster.internal/ubuntu jammy/main riscv64 readline-common all 8.1.2-1 [53.5 kB] Get:124 http://ftpmaster.internal/ubuntu jammy/main riscv64 libreadline8 riscv64 8.1.2-1 [130 kB] Get:125 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsqlite3-0 riscv64 3.37.2-2 [559 kB] Get:126 http://ftpmaster.internal/ubuntu jammy/main riscv64 tzdata all 2021e-1ubuntu1 [343 kB] Get:127 http://ftpmaster.internal/ubuntu jammy/main riscv64 dpkg-dev all 1.21.1ubuntu1 [922 kB] Get:128 http://ftpmaster.internal/ubuntu jammy/main riscv64 libdpkg-perl all 1.21.1ubuntu1 [236 kB] Get:129 http://ftpmaster.internal/ubuntu jammy/main riscv64 make riscv64 4.3-4.1build1 [165 kB] Get:130 http://ftpmaster.internal/ubuntu jammy/main riscv64 lto-disabled-list all 23 [12.5 kB] Get:131 http://ftpmaster.internal/ubuntu jammy/main riscv64 libfakeroot riscv64 1.28-1ubuntu1 [28.0 kB] Get:132 http://ftpmaster.internal/ubuntu jammy/main riscv64 fakeroot riscv64 1.28-1ubuntu1 [68.1 kB] Get:133 http://ftpmaster.internal/ubuntu jammy/main riscv64 gpg riscv64 2.2.27-3ubuntu1 [488 kB] Get:134 http://ftpmaster.internal/ubuntu jammy/main riscv64 gpgconf riscv64 2.2.27-3ubuntu1 [115 kB] Get:135 http://ftpmaster.internal/ubuntu jammy/main riscv64 gpg-agent riscv64 2.2.27-3ubuntu1 [231 kB] Get:136 http://ftpmaster.internal/ubuntu jammy/main riscv64 lockfile-progs riscv64 0.1.19 [9330 B] Get:137 http://ftpmaster.internal/ubuntu jammy/main riscv64 pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 89.8 MB in 18s (4861 kB/s) (Reading database ... 13170 files and directories currently installed.) Preparing to unpack .../libcrypt-dev_1%3a4.4.27-1_riscv64.deb ... Unpacking libcrypt-dev:riscv64 (1:4.4.27-1) over (1:4.4.18-4ubuntu2) ... Preparing to unpack .../libc6-dev_2.35-0ubuntu3_riscv64.deb ... Unpacking libc6-dev:riscv64 (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Preparing to unpack .../libc-dev-bin_2.35-0ubuntu3_riscv64.deb ... Unpacking libc-dev-bin (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Preparing to unpack .../libaudit-common_1%3a3.0.7-1_all.deb ... Unpacking libaudit-common (1:3.0.7-1) over (1:3.0-2ubuntu3) ... Setting up libaudit-common (1:3.0.7-1) ... (Reading database ... 13175 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.9-2.2build3_riscv64.deb ... Unpacking libcap-ng0:riscv64 (0.7.9-2.2build3) over (0.7.9-2.2build2) ... Setting up libcap-ng0:riscv64 (0.7.9-2.2build3) ... (Reading database ... 13175 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0.7-1_riscv64.deb ... Unpacking libaudit1:riscv64 (1:3.0.7-1) over (1:3.0-2ubuntu3) ... Setting up libaudit1:riscv64 (1:3.0.7-1) ... (Reading database ... 13175 files and directories currently installed.) Preparing to unpack .../perl_5.34.0-3ubuntu1_riscv64.deb ... Unpacking perl (5.34.0-3ubuntu1) over (5.32.1-3ubuntu3) ... Selecting previously unselected package perl-modules-5.34. Preparing to unpack .../perl-modules-5.34_5.34.0-3ubuntu1_all.deb ... Unpacking perl-modules-5.34 (5.34.0-3ubuntu1) ... Selecting previously unselected package libperl5.34:riscv64. Preparing to unpack .../libperl5.34_5.34.0-3ubuntu1_riscv64.deb ... Unpacking libperl5.34:riscv64 (5.34.0-3ubuntu1) ... Preparing to unpack .../perl-base_5.34.0-3ubuntu1_riscv64.deb ... Unpacking perl-base (5.34.0-3ubuntu1) over (5.32.1-3ubuntu3) ... Setting up perl-base (5.34.0-3ubuntu1) ... (Reading database ... 15081 files and directories currently installed.) Preparing to unpack .../bzip2_1.0.8-5_riscv64.deb ... Unpacking bzip2 (1.0.8-5) over (1.0.8-4ubuntu4) ... Preparing to unpack .../libbz2-1.0_1.0.8-5_riscv64.deb ... Unpacking libbz2-1.0:riscv64 (1.0.8-5) over (1.0.8-4ubuntu4) ... Setting up libbz2-1.0:riscv64 (1.0.8-5) ... (Reading database ... 15081 files and directories currently installed.) Preparing to unpack .../libgdbm6_1.23-1_riscv64.deb ... Unpacking libgdbm6:riscv64 (1.23-1) over (1.19-2build1) ... Preparing to unpack .../libgdbm-compat4_1.23-1_riscv64.deb ... Unpacking libgdbm-compat4:riscv64 (1.23-1) over (1.19-2build1) ... Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-2ubuntu8_riscv64.deb ... Unpacking zlib1g:riscv64 (1:1.2.11.dfsg-2ubuntu8) over (1:1.2.11.dfsg-2ubuntu7) ... Setting up zlib1g:riscv64 (1:1.2.11.dfsg-2ubuntu8) ... (Reading database ... 15081 files and directories currently installed.) Preparing to unpack .../debconf_1.5.79ubuntu1_all.deb ... Unpacking debconf (1.5.79ubuntu1) over (1.5.77) ... Setting up debconf (1.5.79ubuntu1) ... (Reading database ... 15080 files and directories currently installed.) Preparing to unpack .../libpam0g_1.4.0-11ubuntu1_riscv64.deb ... Unpacking libpam0g:riscv64 (1.4.0-11ubuntu1) over (1.3.1-5ubuntu11) ... Setting up libpam0g:riscv64 (1.4.0-11ubuntu1) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (Reading database ... 15080 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.27-1_riscv64.deb ... Unpacking libcrypt1:riscv64 (1:4.4.27-1) over (1:4.4.18-4ubuntu2) ... Setting up libcrypt1:riscv64 (1:4.4.27-1) ... (Reading database ... 15080 files and directories currently installed.) Preparing to unpack .../linux-libc-dev_5.15.0-23.23_riscv64.deb ... Unpacking linux-libc-dev:riscv64 (5.15.0-23.23) over (5.13.0-19.19) ... Preparing to unpack .../libc6_2.35-0ubuntu3_riscv64.deb ... Unpacking libc6:riscv64 (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Setting up libc6:riscv64 (2.35-0ubuntu3) ... (Reading database ... 15090 files and directories currently installed.) Preparing to unpack .../libc-bin_2.35-0ubuntu3_riscv64.deb ... Unpacking libc-bin (2.35-0ubuntu3) over (2.34-0ubuntu3) ... Setting up libc-bin (2.35-0ubuntu3) ... Selecting previously unselected package gcc-12-base:riscv64. (Reading database ... 15088 files and directories currently installed.) Preparing to unpack .../gcc-12-base_12-20220313-1ubuntu1_riscv64.deb ... Unpacking gcc-12-base:riscv64 (12-20220313-1ubuntu1) ... Setting up gcc-12-base:riscv64 (12-20220313-1ubuntu1) ... (Reading database ... 15093 files and directories currently installed.) Preparing to unpack .../libgcc-s1_12-20220313-1ubuntu1_riscv64.deb ... Unpacking libgcc-s1:riscv64 (12-20220313-1ubuntu1) over (11.2.0-7ubuntu2) ... Setting up libgcc-s1:riscv64 (12-20220313-1ubuntu1) ... (Reading database ... 15093 files and directories currently installed.) Preparing to unpack .../base-files_12ubuntu2_riscv64.deb ... Unpacking base-files (12ubuntu2) over (12ubuntu1) ... Setting up base-files (12ubuntu2) ... (Reading database ... 15093 files and directories currently installed.) Preparing to unpack .../debianutils_5.5-1ubuntu1_riscv64.deb ... Unpacking debianutils (5.5-1ubuntu1) over (4.11.2build1) ... Setting up debianutils (5.5-1ubuntu1) ... update-alternatives: using /usr/bin/which.debianutils to provide /usr/bin/which (which) in auto mode (Reading database ... 15097 files and directories currently installed.) Preparing to unpack .../bash_5.1-6ubuntu1_riscv64.deb ... Unpacking bash (5.1-6ubuntu1) over (5.1-3ubuntu2) ... Setting up bash (5.1-6ubuntu1) ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode (Reading database ... 15097 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.37.2-4ubuntu3_riscv64.deb ... Unpacking bsdutils (1:2.37.2-4ubuntu3) over (1:2.36.1-8ubuntu1) ... Setting up bsdutils (1:2.37.2-4ubuntu3) ... (Reading database ... 15097 files and directories currently installed.) Preparing to unpack .../coreutils_8.32-4.1ubuntu1_riscv64.deb ... Unpacking coreutils (8.32-4.1ubuntu1) over (8.32-4ubuntu3) ... Setting up coreutils (8.32-4.1ubuntu1) ... (Reading database ... 15097 files and directories currently installed.) Preparing to unpack .../libgpg-error0_1.43-3_riscv64.deb ... Unpacking libgpg-error0:riscv64 (1.43-3) over (1.38-2build2) ... Setting up libgpg-error0:riscv64 (1.43-3) ... (Reading database ... 15097 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.9.4-3ubuntu2_riscv64.deb ... Unpacking libgcrypt20:riscv64 (1.9.4-3ubuntu2) over (1.8.7-5ubuntu2) ... Setting up libgcrypt20:riscv64 (1.9.4-3ubuntu2) ... (Reading database ... 15097 files and directories currently installed.) Preparing to unpack .../libstdc++6_12-20220313-1ubuntu1_riscv64.deb ... Unpacking libstdc++6:riscv64 (12-20220313-1ubuntu1) over (11.2.0-7ubuntu2) ... Setting up libstdc++6:riscv64 (12-20220313-1ubuntu1) ... Selecting previously unselected package libssl3:riscv64. (Reading database ... 15097 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.1-0ubuntu1_riscv64.deb ... Unpacking libssl3:riscv64 (3.0.1-0ubuntu1) ... Setting up libssl3:riscv64 (3.0.1-0ubuntu1) ... (Reading database ... 15108 files and directories currently installed.) Preparing to unpack .../libargon2-1_0~20171227-0.3_riscv64.deb ... Unpacking libargon2-1:riscv64 (0~20171227-0.3) over (0~20171227-0.2build22) ... Preparing to unpack .../libblkid1_2.37.2-4ubuntu3_riscv64.deb ... Unpacking libblkid1:riscv64 (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up libblkid1:riscv64 (2.37.2-4ubuntu3) ... (Reading database ... 15108 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.39-3_riscv64.deb ... Unpacking libpcre2-8-0:riscv64 (10.39-3) over (10.37-0ubuntu2) ... Setting up libpcre2-8-0:riscv64 (10.39-3) ... (Reading database ... 15108 files and directories currently installed.) Preparing to unpack .../libselinux1_3.3-1build1_riscv64.deb ... Unpacking libselinux1:riscv64 (3.3-1build1) over (3.1-3build2) ... Setting up libselinux1:riscv64 (3.3-1build1) ... (Reading database ... 15108 files and directories currently installed.) Preparing to unpack .../libudev1_249.11-0ubuntu1_riscv64.deb ... Unpacking libudev1:riscv64 (249.11-0ubuntu1) over (248.3-1ubuntu8) ... Setting up libudev1:riscv64 (249.11-0ubuntu1) ... (Reading database ... 15108 files and directories currently installed.) Preparing to unpack .../libdevmapper1.02.1_2%3a1.02.175-2.1ubuntu4_riscv64.deb ... Unpacking libdevmapper1.02.1:riscv64 (2:1.02.175-2.1ubuntu4) over (2:1.02.175-2.1ubuntu3) ... Preparing to unpack .../libuuid1_2.37.2-4ubuntu3_riscv64.deb ... Unpacking libuuid1:riscv64 (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up libuuid1:riscv64 (2.37.2-4ubuntu3) ... (Reading database ... 15108 files and directories currently installed.) Preparing to unpack .../libcryptsetup12_2%3a2.4.3-1ubuntu1_riscv64.deb ... Unpacking libcryptsetup12:riscv64 (2:2.4.3-1ubuntu1) over (2:2.3.6-0ubuntu1) ... Preparing to unpack .../libgmp10_2%3a6.2.1+dfsg-3ubuntu1_riscv64.deb ... Unpacking libgmp10:riscv64 (2:6.2.1+dfsg-3ubuntu1) over (2:6.2.1+dfsg-1ubuntu3) ... Setting up libgmp10:riscv64 (2:6.2.1+dfsg-3ubuntu1) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../libunistring2_1.0-1_riscv64.deb ... Unpacking libunistring2:riscv64 (1.0-1) over (0.9.10-6) ... Setting up libunistring2:riscv64 (1.0-1) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.2-2_riscv64.deb ... Unpacking libidn2-0:riscv64 (2.3.2-2) over (2.3.1-1build1) ... Setting up libidn2-0:riscv64 (2.3.2-2) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.2-4_riscv64.deb ... Unpacking libffi8:riscv64 (3.4.2-4) over (3.4.2-1ubuntu5) ... Setting up libffi8:riscv64 (3.4.2-4) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.24.0-6_riscv64.deb ... Unpacking libp11-kit0:riscv64 (0.24.0-6) over (0.23.22-1build1) ... Setting up libp11-kit0:riscv64 (0.24.0-6) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.18.0-4_riscv64.deb ... Unpacking libtasn1-6:riscv64 (4.18.0-4) over (4.16.0-2build1) ... Setting up libtasn1-6:riscv64 (4.18.0-4) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.3-4ubuntu1_riscv64.deb ... Unpacking libgnutls30:riscv64 (3.7.3-4ubuntu1) over (3.7.1-5ubuntu1) ... Setting up libgnutls30:riscv64 (3.7.3-4ubuntu1) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../systemd-sysv_249.11-0ubuntu1_riscv64.deb ... Unpacking systemd-sysv (249.11-0ubuntu1) over (248.3-1ubuntu8) ... Preparing to unpack .../systemd-timesyncd_249.11-0ubuntu1_riscv64.deb ... Unpacking systemd-timesyncd (249.11-0ubuntu1) over (248.3-1ubuntu8) ... Preparing to unpack .../libacl1_2.3.1-1_riscv64.deb ... Unpacking libacl1:riscv64 (2.3.1-1) over (2.2.53-10ubuntu2) ... Setting up libacl1:riscv64 (2.3.1-1) ... (Reading database ... 15111 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.0.4-2ubuntu2_riscv64.deb ... Unpacking libapparmor1:riscv64 (3.0.4-2ubuntu2) over (3.0.3-0ubuntu1) ... Preparing to unpack .../libip4tc2_1.8.7-1ubuntu4_riscv64.deb ... Unpacking libip4tc2:riscv64 (1.8.7-1ubuntu4) over (1.8.7-1ubuntu3) ... Preparing to unpack .../libzstd1_1.4.8+dfsg-3_riscv64.deb ... Unpacking libzstd1:riscv64 (1.4.8+dfsg-3) over (1.4.8+dfsg-2.1build1) ... Setting up libzstd1:riscv64 (1.4.8+dfsg-3) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../libkmod2_29-1ubuntu1_riscv64.deb ... Unpacking libkmod2:riscv64 (29-1ubuntu1) over (28-1ubuntu4) ... Preparing to unpack .../libmount1_2.37.2-4ubuntu3_riscv64.deb ... Unpacking libmount1:riscv64 (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up libmount1:riscv64 (2.37.2-4ubuntu3) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.3-2ubuntu1_riscv64.deb ... Unpacking libseccomp2:riscv64 (2.5.3-2ubuntu1) over (2.5.1-1ubuntu1) ... Preparing to unpack .../login_1%3a4.8.1-2ubuntu2_riscv64.deb ... Unpacking login (1:4.8.1-2ubuntu2) over (1:4.8.1-1ubuntu9) ... Setting up login (1:4.8.1-2ubuntu2) ... (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../util-linux_2.37.2-4ubuntu3_riscv64.deb ... Unpacking util-linux (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up util-linux (2.37.2-4ubuntu3) ... (Reading database ... 15105 files and directories currently installed.) Preparing to unpack .../mount_2.37.2-4ubuntu3_riscv64.deb ... Unpacking mount (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Preparing to unpack .../systemd_249.11-0ubuntu1_riscv64.deb ... Unpacking systemd (249.11-0ubuntu1) over (248.3-1ubuntu8) ... Preparing to unpack .../libsystemd0_249.11-0ubuntu1_riscv64.deb ... Unpacking libsystemd0:riscv64 (249.11-0ubuntu1) over (248.3-1ubuntu8) ... Setting up libsystemd0:riscv64 (249.11-0ubuntu1) ... (Reading database ... 15108 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.1-1_riscv64.deb ... Unpacking libxxhash0:riscv64 (0.8.1-1) over (0.8.0-2build1) ... Setting up libxxhash0:riscv64 (0.8.1-1) ... (Reading database ... 15108 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.4.1_riscv64.deb ... Unpacking libapt-pkg6.0:riscv64 (2.4.1) over (2.3.9) ... Setting up libapt-pkg6.0:riscv64 (2.4.1) ... (Reading database ... 15108 files and directories currently installed.) Preparing to unpack .../dpkg_1.21.1ubuntu1_riscv64.deb ... Unpacking dpkg (1.21.1ubuntu1) over (1.20.9ubuntu2) ... Setting up dpkg (1.21.1ubuntu1) ... Installing new version of config file /etc/cron.daily/dpkg ... Created symlink /etc/systemd/system/timers.target.wants/dpkg-db-backup.timer → /lib/systemd/system/dpkg-db-backup.timer. (Reading database ... 15114 files and directories currently installed.) Preparing to unpack .../dash_0.5.11+git20210903+057cd650a4ed-3_riscv64.deb ... Unpacking dash (0.5.11+git20210903+057cd650a4ed-3) over (0.5.11+git20210120+802ebd4-1build1) ... Setting up dash (0.5.11+git20210903+057cd650a4ed-3) ... (Reading database ... 15114 files and directories currently installed.) Preparing to unpack .../grep_3.7-1_riscv64.deb ... Unpacking grep (3.7-1) over (3.7-0ubuntu1) ... Setting up grep (3.7-1) ... (Reading database ... 15114 files and directories currently installed.) Preparing to unpack .../libncurses6_6.3-2_riscv64.deb ... Unpacking libncurses6:riscv64 (6.3-2) over (6.2+20201114-2build2) ... Preparing to unpack .../libncursesw6_6.3-2_riscv64.deb ... Unpacking libncursesw6:riscv64 (6.3-2) over (6.2+20201114-2build2) ... Preparing to unpack .../libtinfo6_6.3-2_riscv64.deb ... Unpacking libtinfo6:riscv64 (6.3-2) over (6.2+20201114-2build2) ... Setting up libtinfo6:riscv64 (6.3-2) ... (Reading database ... 15113 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.3-2_riscv64.deb ... Unpacking ncurses-bin (6.3-2) over (6.2+20201114-2build2) ... Setting up ncurses-bin (6.3-2) ... (Reading database ... 15113 files and directories currently installed.) Preparing to unpack .../sed_4.8-1ubuntu1_riscv64.deb ... Unpacking sed (4.8-1ubuntu1) over (4.7-1ubuntu2) ... Setting up sed (4.8-1ubuntu1) ... (Reading database ... 15113 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.62_all.deb ... Unpacking init-system-helpers (1.62) over (1.60build1) ... Setting up init-system-helpers (1.62) ... (Reading database ... 15113 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.3-2_all.deb ... Unpacking ncurses-base (6.3-2) over (6.2+20201114-2build2) ... Setting up ncurses-base (6.3-2) ... (Reading database ... 15114 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.01-1ubuntu1_riscv64.deb ... Unpacking sysvinit-utils (3.01-1ubuntu1) over (2.96-7ubuntu2) ... Setting up sysvinit-utils (3.01-1ubuntu1) ... (Reading database ... 15114 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.27-3ubuntu1_riscv64.deb ... Unpacking gpgv (2.2.27-3ubuntu1) over (2.2.20-1ubuntu4) ... Setting up gpgv (2.2.27-3ubuntu1) ... (Reading database ... 15114 files and directories currently installed.) Preparing to unpack .../archives/apt_2.4.1_riscv64.deb ... Unpacking apt (2.4.1) over (2.3.9) ... Setting up apt (2.4.1) ... Installing new version of config file /etc/cron.daily/apt-compat ... Selecting previously unselected package libsepol2:riscv64. (Reading database ... 15110 files and directories currently installed.) Preparing to unpack .../libsepol2_3.3-1_riscv64.deb ... Unpacking libsepol2:riscv64 (3.3-1) ... Setting up libsepol2:riscv64 (3.3-1) ... (Reading database ... 15114 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.3-1build2_all.deb ... Unpacking libsemanage-common (3.3-1build2) over (3.1-1ubuntu3) ... Setting up libsemanage-common (3.3-1build2) ... Selecting previously unselected package libsemanage2:riscv64. (Reading database ... 15114 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.3-1build2_riscv64.deb ... Unpacking libsemanage2:riscv64 (3.3-1build2) ... Setting up libsemanage2:riscv64 (3.3-1build2) ... (Reading database ... 15118 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.8.1-2ubuntu2_riscv64.deb ... Unpacking passwd (1:4.8.1-2ubuntu2) over (1:4.8.1-1ubuntu9) ... Setting up passwd (1:4.8.1-2ubuntu2) ... (Reading database ... 15125 files and directories currently installed.) Removing libsemanage1:riscv64 (3.1-1ubuntu3) ... (Reading database ... 15121 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.4.0-11ubuntu1_riscv64.deb ... Unpacking libpam-modules-bin (1.4.0-11ubuntu1) over (1.3.1-5ubuntu11) ... Setting up libpam-modules-bin (1.4.0-11ubuntu1) ... (Reading database ... 15119 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.4.0-11ubuntu1_riscv64.deb ... Unpacking libpam-modules:riscv64 (1.4.0-11ubuntu1) over (1.3.1-5ubuntu11) ... Setting up libpam-modules:riscv64 (1.4.0-11ubuntu1) ... Installing new version of config file /etc/security/namespace.conf ... Installing new version of config file /etc/security/pam_env.conf ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../logsave_1.46.5-2ubuntu1_riscv64.deb ... Unpacking logsave (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Preparing to unpack .../libext2fs2_1.46.5-2ubuntu1_riscv64.deb ... Unpacking libext2fs2:riscv64 (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Setting up libext2fs2:riscv64 (1.46.5-2ubuntu1) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.46.5-2ubuntu1_riscv64.deb ... Unpacking e2fsprogs (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Setting up libapparmor1:riscv64 (3.0.4-2ubuntu2) ... Setting up libargon2-1:riscv64 (0~20171227-0.3) ... Setting up libdevmapper1.02.1:riscv64 (2:1.02.175-2.1ubuntu4) ... Setting up libcryptsetup12:riscv64 (2:2.4.3-1ubuntu1) ... Setting up libip4tc2:riscv64 (1.8.7-1ubuntu4) ... Setting up libkmod2:riscv64 (29-1ubuntu1) ... Setting up libseccomp2:riscv64 (2.5.3-2ubuntu1) ... Setting up mount (2.37.2-4ubuntu3) ... Setting up systemd (249.11-0ubuntu1) ... Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Initializing machine ID from random generator. Setting up systemd-sysv (249.11-0ubuntu1) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../archives/init_1.62_riscv64.deb ... Unpacking init (1.62) over (1.60build1) ... Preparing to unpack .../libattr1_1%3a2.5.1-1_riscv64.deb ... Unpacking libattr1:riscv64 (1:2.5.1-1) over (1:2.4.48-6build2) ... Setting up libattr1:riscv64 (1:2.5.1-1) ... Installing new version of config file /etc/xattr.conf ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../libcom-err2_1.46.5-2ubuntu1_riscv64.deb ... Unpacking libcom-err2:riscv64 (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Setting up libcom-err2:riscv64 (1.46.5-2ubuntu1) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.261ubuntu1_riscv64.deb ... Unpacking libdebconfclient0:riscv64 (0.261ubuntu1) over (0.256ubuntu4) ... Setting up libdebconfclient0:riscv64 (0.261ubuntu1) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../libk5crypto3_1.19.2-2_riscv64.deb ... Unpacking libk5crypto3:riscv64 (1.19.2-2) over (1.18.3-6) ... Setting up libk5crypto3:riscv64 (1.19.2-2) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../libkrb5support0_1.19.2-2_riscv64.deb ... Unpacking libkrb5support0:riscv64 (1.19.2-2) over (1.18.3-6) ... Setting up libkrb5support0:riscv64 (1.19.2-2) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../libkrb5-3_1.19.2-2_riscv64.deb ... Unpacking libkrb5-3:riscv64 (1.19.2-2) over (1.18.3-6) ... Setting up libkrb5-3:riscv64 (1.19.2-2) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../libgssapi-krb5-2_1.19.2-2_riscv64.deb ... Unpacking libgssapi-krb5-2:riscv64 (1.19.2-2) over (1.18.3-6) ... Setting up libgssapi-krb5-2:riscv64 (1.19.2-2) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../libkeyutils1_1.6.1-2ubuntu3_riscv64.deb ... Unpacking libkeyutils1:riscv64 (1.6.1-2ubuntu3) over (1.6.1-2ubuntu2) ... Setting up libkeyutils1:riscv64 (1.6.1-2ubuntu3) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.4.0-11ubuntu1_all.deb ... Unpacking libpam-runtime (1.4.0-11ubuntu1) over (1.3.1-5ubuntu11) ... Setting up libpam-runtime (1.4.0-11ubuntu1) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.37.2-4ubuntu3_riscv64.deb ... Unpacking libsmartcols1:riscv64 (2.37.2-4ubuntu3) over (2.36.1-8ubuntu1) ... Setting up libsmartcols1:riscv64 (2.37.2-4ubuntu3) ... (Reading database ... 15120 files and directories currently installed.) Preparing to unpack .../00-libgomp1_12-20220313-1ubuntu1_riscv64.deb ... Unpacking libgomp1:riscv64 (12-20220313-1ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../01-libatomic1_12-20220313-1ubuntu1_riscv64.deb ... Unpacking libatomic1:riscv64 (12-20220313-1ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../02-libasan6_11.2.0-18ubuntu1_riscv64.deb ... Unpacking libasan6:riscv64 (11.2.0-18ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../03-g++-11_11.2.0-18ubuntu1_riscv64.deb ... Unpacking g++-11 (11.2.0-18ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../04-gcc-11_11.2.0-18ubuntu1_riscv64.deb ... Unpacking gcc-11 (11.2.0-18ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../05-libstdc++-11-dev_11.2.0-18ubuntu1_riscv64.deb ... Unpacking libstdc++-11-dev:riscv64 (11.2.0-18ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../06-libgcc-11-dev_11.2.0-18ubuntu1_riscv64.deb ... Unpacking libgcc-11-dev:riscv64 (11.2.0-18ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../07-libisl23_0.24-2_riscv64.deb ... Unpacking libisl23:riscv64 (0.24-2) over (0.24-1build1) ... Preparing to unpack .../08-libmpc3_1.2.1-1_riscv64.deb ... Unpacking libmpc3:riscv64 (1.2.1-1) over (1.2.0-1build2) ... Preparing to unpack .../09-libcc1-0_12-20220313-1ubuntu1_riscv64.deb ... Unpacking libcc1-0:riscv64 (12-20220313-1ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../10-libctf0_2.38-3ubuntu1_riscv64.deb ... Unpacking libctf0:riscv64 (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../11-libctf-nobfd0_2.38-3ubuntu1_riscv64.deb ... Unpacking libctf-nobfd0:riscv64 (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../12-binutils-riscv64-linux-gnu_2.38-3ubuntu1_riscv64.deb ... Unpacking binutils-riscv64-linux-gnu (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../13-libbinutils_2.38-3ubuntu1_riscv64.deb ... Unpacking libbinutils:riscv64 (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../14-binutils_2.38-3ubuntu1_riscv64.deb ... Unpacking binutils (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../15-binutils-common_2.38-3ubuntu1_riscv64.deb ... Unpacking binutils-common:riscv64 (2.38-3ubuntu1) over (2.37-7ubuntu1) ... Preparing to unpack .../16-cpp-11_11.2.0-18ubuntu1_riscv64.deb ... Unpacking cpp-11 (11.2.0-18ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../17-gcc-11-base_11.2.0-18ubuntu1_riscv64.deb ... Unpacking gcc-11-base:riscv64 (11.2.0-18ubuntu1) over (11.2.0-7ubuntu2) ... Preparing to unpack .../18-libprocps8_2%3a3.3.17-6ubuntu2_riscv64.deb ... Unpacking libprocps8:riscv64 (2:3.3.17-6ubuntu2) over (2:3.3.17-5ubuntu3) ... Preparing to unpack .../19-libss2_1.46.5-2ubuntu1_riscv64.deb ... Unpacking libss2:riscv64 (1.46.5-2ubuntu1) over (1.46.3-1ubuntu3) ... Preparing to unpack .../20-mawk_1.3.4.20200120-3_riscv64.deb ... Unpacking mawk (1.3.4.20200120-3) over (1.3.4.20200120-2build1) ... Preparing to unpack .../21-procps_2%3a3.3.17-6ubuntu2_riscv64.deb ... Unpacking procps (2:3.3.17-6ubuntu2) over (2:3.3.17-5ubuntu3) ... Preparing to unpack .../22-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) over (0.0.14) ... Preparing to unpack .../23-usrmerge_25ubuntu2_all.deb ... Unpacking usrmerge (25ubuntu2) over (25ubuntu1) ... Preparing to unpack .../24-openssl_3.0.1-0ubuntu1_riscv64.deb ... Unpacking openssl (3.0.1-0ubuntu1) over (1.1.1l-1ubuntu1) ... Preparing to unpack .../25-ca-certificates_20211016_all.deb ... Unpacking ca-certificates (20211016) over (20210119ubuntu1) ... Preparing to unpack .../26-readline-common_8.1.2-1_all.deb ... Unpacking readline-common (8.1.2-1) over (8.1-2build1) ... Preparing to unpack .../27-libreadline8_8.1.2-1_riscv64.deb ... Unpacking libreadline8:riscv64 (8.1.2-1) over (8.1-2build1) ... Preparing to unpack .../28-libsqlite3-0_3.37.2-2_riscv64.deb ... Unpacking libsqlite3-0:riscv64 (3.37.2-2) over (3.35.5-1) ... Preparing to unpack .../29-tzdata_2021e-1ubuntu1_all.deb ... Unpacking tzdata (2021e-1ubuntu1) over (2021a-2ubuntu1) ... Preparing to unpack .../30-dpkg-dev_1.21.1ubuntu1_all.deb ... Unpacking dpkg-dev (1.21.1ubuntu1) over (1.20.9ubuntu2) ... Preparing to unpack .../31-libdpkg-perl_1.21.1ubuntu1_all.deb ... Unpacking libdpkg-perl (1.21.1ubuntu1) over (1.20.9ubuntu2) ... Preparing to unpack .../32-make_4.3-4.1build1_riscv64.deb ... Unpacking make (4.3-4.1build1) over (4.3-4ubuntu1) ... Preparing to unpack .../33-lto-disabled-list_23_all.deb ... Unpacking lto-disabled-list (23) over (16) ... Preparing to unpack .../34-libfakeroot_1.28-1ubuntu1_riscv64.deb ... Unpacking libfakeroot:riscv64 (1.28-1ubuntu1) over (1.25.3-1.1ubuntu3) ... Preparing to unpack .../35-fakeroot_1.28-1ubuntu1_riscv64.deb ... Unpacking fakeroot (1.28-1ubuntu1) over (1.25.3-1.1ubuntu3) ... Preparing to unpack .../36-gpg_2.2.27-3ubuntu1_riscv64.deb ... Unpacking gpg (2.2.27-3ubuntu1) over (2.2.20-1ubuntu4) ... Preparing to unpack .../37-gpgconf_2.2.27-3ubuntu1_riscv64.deb ... Unpacking gpgconf (2.2.27-3ubuntu1) over (2.2.20-1ubuntu4) ... Preparing to unpack .../38-gpg-agent_2.2.27-3ubuntu1_riscv64.deb ... Unpacking gpg-agent (2.2.27-3ubuntu1) over (2.2.20-1ubuntu4) ... Preparing to unpack .../39-lockfile-progs_0.1.19_riscv64.deb ... Unpacking lockfile-progs (0.1.19) over (0.1.18build1) ... Preparing to unpack .../40-pkgbinarymangler_149_all.deb ... Unpacking pkgbinarymangler (149) over (148) ... Setting up gcc-11-base:riscv64 (11.2.0-18ubuntu1) ... Setting up lto-disabled-list (23) ... Setting up init (1.62) ... Setting up libsqlite3-0:riscv64 (3.37.2-2) ... Setting up binutils-common:riscv64 (2.38-3ubuntu1) ... Setting up linux-libc-dev:riscv64 (5.15.0-23.23) ... Setting up libctf-nobfd0:riscv64 (2.38-3ubuntu1) ... Setting up libgomp1:riscv64 (12-20220313-1ubuntu1) ... Setting up perl-modules-5.34 (5.34.0-3ubuntu1) ... Setting up bzip2 (1.0.8-5) ... Setting up libfakeroot:riscv64 (1.28-1ubuntu1) ... Setting up libasan6:riscv64 (11.2.0-18ubuntu1) ... Setting up tzdata (2021e-1ubuntu1) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Mar 17 17:20:31 UTC 2022. Universal Time is now: Thu Mar 17 17:20:31 UTC 2022. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up fakeroot (1.28-1ubuntu1) ... Setting up make (4.3-4.1build1) ... Setting up libncurses6:riscv64 (6.3-2) ... Setting up libmpc3:riscv64 (1.2.1-1) ... Setting up systemd-timesyncd (249.11-0ubuntu1) ... Setting up lockfile-progs (0.1.19) ... Setting up libatomic1:riscv64 (12-20220313-1ubuntu1) ... Setting up usrmerge (25ubuntu2) ... Setting up libss2:riscv64 (1.46.5-2ubuntu1) ... Setting up libncursesw6:riscv64 (6.3-2) ... Setting up logsave (1.46.5-2ubuntu1) ... Setting up libgcc-11-dev:riscv64 (11.2.0-18ubuntu1) ... Setting up sensible-utils (0.0.17) ... Setting up libcrypt-dev:riscv64 (1:4.4.27-1) ... Setting up mawk (1.3.4.20200120-3) ... Setting up libbinutils:riscv64 (2.38-3ubuntu1) ... Setting up libisl23:riscv64 (0.24-2) ... Setting up libc-dev-bin (2.35-0ubuntu3) ... Setting up openssl (3.0.1-0ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.1.2-1) ... Setting up libcc1-0:riscv64 (12-20220313-1ubuntu1) ... Setting up libprocps8:riscv64 (2:3.3.17-6ubuntu2) ... Setting up libgdbm6:riscv64 (1.23-1) ... Setting up libctf0:riscv64 (2.38-3ubuntu1) ... Setting up cpp-11 (11.2.0-18ubuntu1) ... Setting up pkgbinarymangler (149) ... Setting up libreadline8:riscv64 (8.1.2-1) ... Setting up binutils-riscv64-linux-gnu (2.38-3ubuntu1) ... Setting up e2fsprogs (1.46.5-2ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up binutils (2.38-3ubuntu1) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up libgdbm-compat4:riscv64 (1.23-1) ... Setting up gcc-11 (11.2.0-18ubuntu1) ... Setting up procps (2:3.3.17-6ubuntu2) ... Installing new version of config file /etc/init.d/procps ... Installing new version of config file /etc/sysctl.d/README.sysctl ... Setting up gpgconf (2.2.27-3ubuntu1) ... Setting up libc6-dev:riscv64 (2.35-0ubuntu3) ... Setting up gpg (2.2.27-3ubuntu1) ... Setting up libperl5.34:riscv64 (5.34.0-3ubuntu1) ... Setting up gpg-agent (2.2.27-3ubuntu1) ... Setting up perl (5.34.0-3ubuntu1) ... Setting up libdpkg-perl (1.21.1ubuntu1) ... Setting up libstdc++-11-dev:riscv64 (11.2.0-18ubuntu1) ... Setting up g++-11 (11.2.0-18ubuntu1) ... Setting up dpkg-dev (1.21.1ubuntu1) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-23248863 riscv64 jammy-proposed -c chroot:build-PACKAGEBUILD-23248863 --arch=riscv64 --dist=jammy-proposed --nolog ariba_2.14.6+ds-3build1.dsc Initiating build PACKAGEBUILD-23248863 with 8 jobs across 8 processor cores. Kernel reported to sbuild: 5.11.0-1029-generic #32~20.04.1-Ubuntu SMP Fri Jan 28 13:38:22 UTC 2022 riscv64 sbuild (Debian sbuild) 0.79.0 (05 February 2020) on riscv64-qemu-lcy01-007.buildd +==============================================================================+ | ariba 2.14.6+ds-3build1 (riscv64) Thu, 17 Mar 2022 17:22:52 +0000 | +==============================================================================+ Package: ariba Version: 2.14.6+ds-3build1 Source Version: 2.14.6+ds-3build1 Distribution: jammy-proposed Machine Architecture: riscv64 Host Architecture: riscv64 Build Architecture: riscv64 Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-23248863/chroot-autobuild' with '<>' I: NOTICE: Log filtering will replace 'build/ariba-01Tyry/resolver-QpH12f' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- ariba_2.14.6+ds-3build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/ariba-01Tyry/ariba-2.14.6+ds' with '<>' I: NOTICE: Log filtering will replace 'build/ariba-01Tyry' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), dh-python, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3-pytest, 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, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3-pytest, 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, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [540 B] Get:5 copy:/<>/apt_archive ./ Packages [605 B] Fetched 2102 B in 1s (2877 B/s) Reading package lists... Reading package lists... Install main 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: libperl5.32 libssl1.1 perl-modules-5.32 systemd-timesyncd Use 'apt autoremove' to remove them. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev blt bowtie2 bsdextrautils cd-hit debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 gawk gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcapnp-0.8.0 libcurl3-gnutls libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libicu70 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libmd0 libminimap-dev libminimap0 libmpdec3 libmurmurhash2 libnghttp2-14 libopenjp2-7 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libraqm0 librtmp1 libruby3.0 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libyaml-0-2 m4 mailcap man-db mash media-types mime-support mummer po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-biopython python3-brotli python3-bs4 python3-cycler python3-dateutil python3-decorator python3-dendropy python3-dev python3-distutils python3-fonttools python3-fs python3-importlib-metadata python3-iniconfig python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-py python3-pymummer python3-pyparsing python3-pysam python3-pytest python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-soupsieve python3-sympy python3-tk python3-toml python3-tz python3-ufolib2 python3-unicodedata2 python3-zipp python3.10 python3.10-dev python3.10-minimal rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-xmlrpc ruby3.0 rubygems-integration samtools sgml-base tk8.6-blt2.5 ucf unicode-data w3-dtd-mathml x11-common xml-core zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc blt-demo bowtie2-examples dh-make flit python3-build python3-tomli python3-installer fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gawk-doc gettext-doc libasprintf-dev libgettextpo-dev groff gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html 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 python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-psycopg2 raxml t-coffee wise python-cycler-doc python-lxml-doc dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gfortran python-numpy-doc python-pil-doc subversion python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python-setuptools-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.10-venv python3.10-doc binfmt-support ri ruby-dev bundler cwltool sgml-base-doc docbook-mathml Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl python-biopython-doc ncbi-blast+ python3-chardet python3-html5lib python3-olefile python3-pygments zip fonts-lato The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev blt bowtie2 bsdextrautils cd-hit debhelper debugedit dh-autoreconf dh-python dh-strip-nondeterminism dwz fastaq file fontconfig-config fonts-dejavu-core fonts-lyx fonts-urw-base35 gawk gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libblas3 libbrotli1 libbsd0 libcapnp-0.8.0 libcurl3-gnutls libdebhelper-perl libdeflate0 libdw1 libedit2 libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgsl27 libgslcblas0 libharfbuzz0b libhts3 libhtscodecs2 libicu70 libimagequant0 libjbig0 libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblocale-gettext-perl libmagic-mgc libmagic1 libmd0 libminimap-dev libminimap0 libmpdec3 libmurmurhash2 libnghttp2-14 libopenjp2-7 libpipeline1 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.10 libpython3.10-dev libpython3.10-minimal libpython3.10-stdlib libqhull-r8.0 libraqm0 librtmp1 libruby3.0 libsasl2-2 libsasl2-modules-db libsigsegv2 libssh-4 libsub-override-perl libtcl8.6 libtiff5 libtk8.6 libtool libuchardet0 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 libyaml-0-2 m4 mailcap man-db mash media-types mime-support mummer po-debconf python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-biopython python3-brotli python3-bs4 python3-cycler python3-dateutil python3-decorator python3-dendropy python3-dev python3-distutils python3-fonttools python3-fs python3-importlib-metadata python3-iniconfig python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pluggy python3-py python3-pymummer python3-pyparsing python3-pysam python3-pytest python3-renderpm python3-reportlab python3-reportlab-accel python3-scipy python3-setuptools python3-six python3-soupsieve python3-sympy python3-tk python3-toml python3-tz python3-ufolib2 python3-unicodedata2 python3-zipp python3.10 python3.10-dev python3.10-minimal rake ruby ruby-asciidoctor ruby-net-telnet ruby-rubygems ruby-xmlrpc ruby3.0 rubygems-integration samtools sbuild-build-depends-main-dummy sgml-base tk8.6-blt2.5 ucf unicode-data w3-dtd-mathml x11-common xml-core zlib1g-dev 0 upgraded, 196 newly installed, 0 to remove and 0 not upgraded. Need to get 119 MB of archives. After this operation, 487 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [832 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main riscv64 liblocale-gettext-perl riscv64 1.07-4build3 [16.4 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libpython3.10-minimal riscv64 3.10.3-1 [793 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main riscv64 libexpat1 riscv64 2.4.7-1 [85.2 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 python3.10-minimal riscv64 3.10.3-1 [1732 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-minimal riscv64 3.10.1-0ubuntu2 [24.6 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main riscv64 media-types all 6.0.0 [25.6 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main riscv64 mailcap all 3.70+nmu1ubuntu1 [23.8 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main riscv64 mime-support all 3.66 [3696 B] Get:10 http://ftpmaster.internal/ubuntu jammy/main riscv64 libmpdec3 riscv64 2.5.1-2build1 [84.9 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libpython3.10-stdlib riscv64 3.10.3-1 [1717 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 python3.10 riscv64 3.10.3-1 [487 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpython3-stdlib riscv64 3.10.1-0ubuntu2 [7222 B] Get:14 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3 riscv64 3.10.1-0ubuntu2 [22.8 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsigsegv2 riscv64 2.13-1ubuntu2 [13.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main riscv64 gawk riscv64 1:5.1.0-1build2 [410 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main riscv64 sgml-base all 1.30 [12.5 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main riscv64 libmd0 riscv64 1.0.4-1 [30.0 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main riscv64 libbsd0 riscv64 0.11.5-1 [40.9 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main riscv64 libelf1 riscv64 0.186-1 [46.6 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main riscv64 libfribidi0 riscv64 1.0.8-2ubuntu2 [25.3 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main riscv64 libglib2.0-0 riscv64 2.71.3-1 [1310 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main riscv64 libicu70 riscv64 70.1-2 [10.5 MB] Get:24 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxml2 riscv64 2.9.13+dfsg-1 [605 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main riscv64 libyaml-0-2 riscv64 0.2.2-1build1 [49.4 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-pkg-resources all 59.6.0-1.2 [132 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main riscv64 ucf all 3.0043 [56.1 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main riscv64 bsdextrautils riscv64 2.37.2-4ubuntu3 [81.5 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main riscv64 libmagic-mgc riscv64 1:5.41-2 [257 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main riscv64 libmagic1 riscv64 1:5.41-2 [88.6 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main riscv64 file riscv64 1:5.41-2 [20.5 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main riscv64 gettext-base riscv64 0.21-4ubuntu3 [37.2 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main riscv64 libuchardet0 riscv64 0.0.7-1build1 [78.9 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main riscv64 groff-base riscv64 1.22.4-8 [922 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main riscv64 libedit2 riscv64 3.1-20210910-1 [81.8 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpipeline1 riscv64 1.5.5-1 [26.2 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpsl5 riscv64 0.21.0-1.2build1 [56.4 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxau6 riscv64 1:1.0.9-1build4 [6784 B] Get:39 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxdmcp6 riscv64 1:1.1.3-0ubuntu4 [10.4 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxcb1 riscv64 1.14-3ubuntu2 [42.6 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main riscv64 libx11-data all 2:1.7.2-2 [123 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main riscv64 libx11-6 riscv64 2:1.7.2-2 [619 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxext6 riscv64 2:1.3.4-1 [27.7 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main riscv64 man-db riscv64 2.10.1-1 [1143 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main riscv64 rubygems-integration all 1.18 [5336 B] Get:46 http://ftpmaster.internal/ubuntu jammy/main riscv64 rake all 13.0.6-2 [61.7 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main riscv64 ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main riscv64 ruby-xmlrpc all 0.3.2-1 [24.6 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libruby3.0 riscv64 3.0.2-7ubuntu1 [4915 kB] Get:50 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 ruby3.0 riscv64 3.0.2-7ubuntu1 [50.0 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main riscv64 ruby-rubygems all 3.3.5-2 [228 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main riscv64 ruby riscv64 1:3.0~exp1 [5096 B] Get:53 http://ftpmaster.internal/ubuntu jammy/universe riscv64 ruby-asciidoctor all 2.0.16-2 [173 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/universe riscv64 asciidoctor all 2.0.16-2 [44.3 kB] Get:55 http://ftpmaster.internal/ubuntu jammy/main riscv64 m4 riscv64 1.4.18-5ubuntu1 [193 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main riscv64 autoconf all 2.71-2 [338 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main riscv64 autotools-dev all 20220109.1 [44.9 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main riscv64 automake all 1:1.16.5-1.1ubuntu4 [558 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main riscv64 autopoint all 0.21-4ubuntu3 [422 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main riscv64 libtcl8.6 riscv64 8.6.12+dfsg-1 [937 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main riscv64 libbrotli1 riscv64 1.0.9-2build4 [330 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main riscv64 libfreetype6 riscv64 2.11.1+dfsg-1 [361 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main riscv64 fonts-dejavu-core all 2.37-2build1 [1041 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main riscv64 fonts-urw-base35 all 20200910-1 [6367 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main riscv64 fontconfig-config all 2.13.1-4.2ubuntu4 [29.1 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main riscv64 libfontconfig1 riscv64 2.13.1-4.2ubuntu4 [116 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxrender1 riscv64 1:0.9.10-1build3 [17.2 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxft2 riscv64 2.3.3-0ubuntu4 [36.7 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main riscv64 x11-common all 1:7.7+23ubuntu1 [23.5 kB] Get:70 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxss1 riscv64 1:1.2.3-1build1 [7654 B] Get:71 http://ftpmaster.internal/ubuntu jammy/main riscv64 libtk8.6 riscv64 8.6.12-1 [701 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main riscv64 tk8.6-blt2.5 riscv64 2.5.3+dfsg-4.1build1 [549 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main riscv64 blt riscv64 2.5.3+dfsg-4.1build1 [4846 B] Get:74 http://ftpmaster.internal/ubuntu jammy/universe riscv64 cd-hit riscv64 4.8.1-4 [529 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main riscv64 libdebhelper-perl all 13.6ubuntu1 [67.2 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main riscv64 libtool all 2.4.6-15build1 [164 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main riscv64 dh-autoreconf all 20 [16.1 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsub-override-perl all 0.09-2 [9532 B] Get:80 http://ftpmaster.internal/ubuntu jammy/main riscv64 libfile-stripnondeterminism-perl all 1.13.0-1 [18.1 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/main riscv64 dh-strip-nondeterminism all 1.13.0-1 [5344 B] Get:82 http://ftpmaster.internal/ubuntu jammy/main riscv64 libdw1 riscv64 0.186-1 [228 kB] Get:83 http://ftpmaster.internal/ubuntu jammy/main riscv64 debugedit riscv64 1:5.0-4 [49.8 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main riscv64 dwz riscv64 0.14-1build1 [105 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/main riscv64 gettext riscv64 0.21-4ubuntu3 [769 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main riscv64 intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:87 http://ftpmaster.internal/ubuntu jammy/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main riscv64 debhelper all 13.6ubuntu1 [923 kB] Get:89 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 python3-lib2to3 all 3.10.3-0ubuntu2 [76.1 kB] Get:90 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 python3-distutils all 3.10.3-0ubuntu2 [138 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/universe riscv64 dh-python all 5.20220215 [104 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsasl2-modules-db riscv64 2.1.27+dfsg2-3ubuntu1 [19.5 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main riscv64 libsasl2-2 riscv64 2.1.27+dfsg2-3ubuntu1 [53.3 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main riscv64 libldap-2.5-0 riscv64 2.5.11+dfsg-1~exp1ubuntu3 [163 kB] Get:95 http://ftpmaster.internal/ubuntu jammy/main riscv64 libnghttp2-14 riscv64 1.43.0-1build2 [73.3 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main riscv64 librtmp1 riscv64 2.4+20151223.gitfa8646d.1-2build3 [54.7 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main riscv64 libssh-4 riscv64 0.9.6-2 [162 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcurl3-gnutls riscv64 7.81.0-1 [249 kB] Get:99 http://ftpmaster.internal/ubuntu jammy/main riscv64 libdeflate0 riscv64 1.10-1ubuntu1 [68.1 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libhtscodecs2 riscv64 1.1.1-3 [62.1 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libhts3 riscv64 1.13+ds-2build1 [353 kB] Get:102 http://ftpmaster.internal/ubuntu jammy/universe riscv64 samtools riscv64 1.13-4 [548 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/universe riscv64 fastaq all 3.17.0-4 [48.3 kB] Get:104 http://ftpmaster.internal/ubuntu jammy/universe riscv64 fonts-lyx all 2.3.6-1 [159 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/universe riscv64 help2man riscv64 1.49.1 [186 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main riscv64 libblas3 riscv64 3.10.0-2ubuntu1 [123 kB] Get:107 http://ftpmaster.internal/ubuntu jammy/main riscv64 libcapnp-0.8.0 riscv64 0.8.0-2ubuntu2 [1205 kB] Get:108 http://ftpmaster.internal/ubuntu jammy/main riscv64 libexpat1-dev riscv64 2.4.7-1 [331 kB] Get:109 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libfml0 riscv64 0.1+git20190320.b499514-1 [68.4 kB] Get:110 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 zlib1g-dev riscv64 1:1.2.11.dfsg-2ubuntu8 [241 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libfml-dev riscv64 0.1+git20190320.b499514-1 [163 kB] Get:112 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgfortran5 riscv64 12-20220313-1ubuntu1 [376 kB] Get:113 http://ftpmaster.internal/ubuntu jammy/main riscv64 libgraphite2-3 riscv64 1.3.14-1build1 [71.5 kB] Get:114 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libgslcblas0 riscv64 2.7.1+dfsg-3 [80.0 kB] Get:115 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libgsl27 riscv64 2.7.1+dfsg-3 [996 kB] Get:116 http://ftpmaster.internal/ubuntu jammy/main riscv64 libharfbuzz0b riscv64 2.7.4-1ubuntu3 [369 kB] Get:117 http://ftpmaster.internal/ubuntu jammy/main riscv64 libimagequant0 riscv64 2.17.0-1 [32.1 kB] Get:118 http://ftpmaster.internal/ubuntu jammy/main riscv64 libjpeg-turbo8 riscv64 2.1.2-0ubuntu1 [113 kB] Get:119 http://ftpmaster.internal/ubuntu jammy/main riscv64 libjpeg8 riscv64 8c-2ubuntu8 [2224 B] Get:120 http://ftpmaster.internal/ubuntu jammy/main riscv64 libjs-jquery all 3.6.0+dfsg+~3.5.13-1 [321 kB] Get:121 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libjs-jquery-ui all 1.13.1+dfsg-1 [253 kB] Get:122 http://ftpmaster.internal/ubuntu jammy/main riscv64 libjs-underscore all 1.13.2~dfsg-2 [118 kB] Get:123 http://ftpmaster.internal/ubuntu jammy/main riscv64 libjs-sphinxdoc all 4.3.2-1 [139 kB] Get:124 http://ftpmaster.internal/ubuntu jammy/main riscv64 liblapack3 riscv64 3.10.0-2ubuntu1 [1902 kB] Get:125 http://ftpmaster.internal/ubuntu jammy/universe riscv64 liblbfgsb0 riscv64 3.0+dfsg.3-10 [26.4 kB] Get:126 http://ftpmaster.internal/ubuntu jammy/main riscv64 liblcms2-2 riscv64 2.12~rc1-2build1 [143 kB] Get:127 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libminimap0 riscv64 0.2-6 [20.7 kB] Get:128 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libminimap-dev riscv64 0.2-6 [59.3 kB] Get:129 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libmurmurhash2 riscv64 1.5-3 [6418 B] Get:130 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libpython3.10 riscv64 3.10.3-1 [1759 kB] Get:131 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 libpython3.10-dev riscv64 3.10.3-1 [12.9 MB] Get:132 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpython3-dev riscv64 3.10.1-0ubuntu2 [7486 B] Get:133 http://ftpmaster.internal/ubuntu jammy/main riscv64 libpython3-all-dev riscv64 3.10.1-0ubuntu2 [926 B] Get:134 http://ftpmaster.internal/ubuntu jammy/universe riscv64 libqhull-r8.0 riscv64 2020.2-4 [182 kB] Get:135 http://ftpmaster.internal/ubuntu jammy/main riscv64 libraqm0 riscv64 0.7.0-4ubuntu1 [10.4 kB] Get:136 http://ftpmaster.internal/ubuntu jammy/main riscv64 libjbig0 riscv64 2.1-3.1build2 [27.4 kB] Get:137 http://ftpmaster.internal/ubuntu jammy/main riscv64 libwebp7 riscv64 1.2.2-2 [162 kB] Get:138 http://ftpmaster.internal/ubuntu jammy/main riscv64 libtiff5 riscv64 4.3.0-6 [165 kB] Get:139 http://ftpmaster.internal/ubuntu jammy/main riscv64 libwebpdemux2 riscv64 1.2.2-2 [9062 B] Get:140 http://ftpmaster.internal/ubuntu jammy/main riscv64 libwebpmux3 riscv64 1.2.2-2 [18.2 kB] Get:141 http://ftpmaster.internal/ubuntu jammy/main riscv64 libxslt1.1 riscv64 1.1.34-4build1 [146 kB] Get:142 http://ftpmaster.internal/ubuntu jammy/universe riscv64 mash riscv64 2.3+dfsg-1build2 [201 kB] Get:143 http://ftpmaster.internal/ubuntu jammy/universe riscv64 mummer riscv64 3.23+dfsg-7 [653 kB] Get:144 http://ftpmaster.internal/ubuntu jammy-proposed/universe riscv64 python-matplotlib-data all 3.5.1-2build1 [2942 kB] Get:145 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-all riscv64 3.10.1-0ubuntu2 [916 B] Get:146 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 python3.10-dev riscv64 3.10.3-1 [500 kB] Get:147 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-dev riscv64 3.10.1-0ubuntu2 [26.0 kB] Get:148 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-all-dev riscv64 3.10.1-0ubuntu2 [920 B] Get:149 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-appdirs all 1.4.4-2 [11.4 kB] Get:150 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-attr all 21.2.0-1 [44.0 kB] Get:151 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 python3-numpy riscv64 1:1.21.5-1build1 [3003 kB] Get:152 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-renderpm riscv64 3.6.8-1 [56.7 kB] Get:153 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-reportlab-accel riscv64 3.6.8-1 [18.7 kB] Get:154 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 python3-tk riscv64 3.10.3-0ubuntu2 [99.3 kB] Get:155 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-pil.imagetk riscv64 9.0.1-1 [9032 B] Get:156 http://ftpmaster.internal/ubuntu jammy/main riscv64 libopenjp2-7 riscv64 2.4.0-6 [159 kB] Get:157 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-pil riscv64 9.0.1-1 [421 kB] Get:158 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-reportlab all 3.6.8-1 [559 kB] Get:159 http://ftpmaster.internal/ubuntu jammy/main riscv64 xml-core all 0.18+nmu1 [21.6 kB] Get:160 http://ftpmaster.internal/ubuntu jammy/universe riscv64 w3-dtd-mathml all 2.0.0.0-5.1 [57.3 kB] Get:161 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-biopython riscv64 1.79+dfsg-2 [1450 kB] Get:162 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-brotli riscv64 1.0.9-2build4 [332 kB] Get:163 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-soupsieve all 2.3.1-1 [33.0 kB] Get:164 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-bs4 all 4.10.0-2 [79.1 kB] Get:165 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-cycler all 0.11.0-1 [8156 B] Get:166 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-six all 1.16.0-3 [12.5 kB] Get:167 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-dateutil all 2.8.1-6 [78.4 kB] Get:168 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-decorator all 4.4.2-0ubuntu1 [10.3 kB] Get:169 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-dendropy all 4.5.2-1 [276 kB] Get:170 http://ftpmaster.internal/ubuntu jammy-proposed/universe riscv64 python3-scipy riscv64 1.8.0-1exp2build1 [14.6 MB] Get:171 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-ufolib2 all 0.13.1+dfsg1-1 [32.2 kB] Get:172 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-mpmath all 1.2.1-2 [419 kB] Get:173 http://ftpmaster.internal/ubuntu jammy-proposed/universe riscv64 python3-sympy all 1.9-1 [4312 kB] Get:174 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-tz all 2021.3-1 [33.3 kB] Get:175 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-fs all 2.4.12-1 [84.9 kB] Get:176 http://ftpmaster.internal/ubuntu jammy-proposed/main riscv64 python3-lxml riscv64 4.8.0-1build1 [1047 kB] Get:177 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-lz4 riscv64 3.1.3+dfsg-1build2 [31.3 kB] Get:178 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-unicodedata2 riscv64 14.0.0+ds-8 [377 kB] Get:179 http://ftpmaster.internal/ubuntu jammy/universe riscv64 unicode-data all 14.0.0-1.1 [8206 kB] Get:180 http://ftpmaster.internal/ubuntu jammy-proposed/universe riscv64 python3-fonttools riscv64 4.29.1-2build1 [801 kB] Get:181 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-more-itertools all 8.10.0-2 [47.9 kB] Get:182 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-zipp all 1.0.0-3 [5440 B] Get:183 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-importlib-metadata all 4.6.4-1 [16.2 kB] Get:184 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-iniconfig all 1.1.1-2 [6024 B] Get:185 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-kiwisolver riscv64 1.3.2-1 [72.5 kB] Get:186 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-pyparsing all 2.4.7-1 [61.4 kB] Get:187 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-packaging all 21.3-1 [30.7 kB] Get:188 http://ftpmaster.internal/ubuntu jammy-proposed/universe riscv64 python3-matplotlib riscv64 3.5.1-2build1 [5632 kB] Get:189 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-pluggy all 0.13.0-7.1 [19.0 kB] Get:190 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-py all 1.10.0-1 [71.9 kB] Get:191 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-pymummer all 0.11.0-2 [9976 B] Get:192 http://ftpmaster.internal/ubuntu jammy-proposed/universe riscv64 python3-pysam riscv64 0.17.0+ds-2build1 [1649 kB] Get:193 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-toml all 0.10.2-1 [16.5 kB] Get:194 http://ftpmaster.internal/ubuntu jammy/universe riscv64 python3-pytest all 6.2.5-1ubuntu2 [214 kB] Get:195 http://ftpmaster.internal/ubuntu jammy/main riscv64 python3-setuptools all 59.6.0-1.2 [339 kB] Get:196 http://ftpmaster.internal/ubuntu jammy-proposed/universe riscv64 bowtie2 riscv64 2.4.5-1 [1700 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 119 MB in 24s (4948 kB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 15284 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-4build3_riscv64.deb ... Unpacking liblocale-gettext-perl (1.07-4build3) ... Selecting previously unselected package libpython3.10-minimal:riscv64. Preparing to unpack .../libpython3.10-minimal_3.10.3-1_riscv64.deb ... Unpacking libpython3.10-minimal:riscv64 (3.10.3-1) ... Selecting previously unselected package libexpat1:riscv64. Preparing to unpack .../libexpat1_2.4.7-1_riscv64.deb ... Unpacking libexpat1:riscv64 (2.4.7-1) ... Selecting previously unselected package python3.10-minimal. Preparing to unpack .../python3.10-minimal_3.10.3-1_riscv64.deb ... Unpacking python3.10-minimal (3.10.3-1) ... Setting up libpython3.10-minimal:riscv64 (3.10.3-1) ... Setting up libexpat1:riscv64 (2.4.7-1) ... Setting up python3.10-minimal (3.10.3-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 15600 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.10.1-0ubuntu2_riscv64.deb ... Unpacking python3-minimal (3.10.1-0ubuntu2) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_6.0.0_all.deb ... Unpacking media-types (6.0.0) ... Selecting previously unselected package mailcap. Preparing to unpack .../2-mailcap_3.70+nmu1ubuntu1_all.deb ... Unpacking mailcap (3.70+nmu1ubuntu1) ... Selecting previously unselected package mime-support. Preparing to unpack .../3-mime-support_3.66_all.deb ... Unpacking mime-support (3.66) ... Selecting previously unselected package libmpdec3:riscv64. Preparing to unpack .../4-libmpdec3_2.5.1-2build1_riscv64.deb ... Unpacking libmpdec3:riscv64 (2.5.1-2build1) ... Selecting previously unselected package libpython3.10-stdlib:riscv64. Preparing to unpack .../5-libpython3.10-stdlib_3.10.3-1_riscv64.deb ... Unpacking libpython3.10-stdlib:riscv64 (3.10.3-1) ... Selecting previously unselected package python3.10. Preparing to unpack .../6-python3.10_3.10.3-1_riscv64.deb ... Unpacking python3.10 (3.10.3-1) ... Selecting previously unselected package libpython3-stdlib:riscv64. Preparing to unpack .../7-libpython3-stdlib_3.10.1-0ubuntu2_riscv64.deb ... Unpacking libpython3-stdlib:riscv64 (3.10.1-0ubuntu2) ... Setting up python3-minimal (3.10.1-0ubuntu2) ... Selecting previously unselected package python3. (Reading database ... 16026 files and directories currently installed.) Preparing to unpack .../python3_3.10.1-0ubuntu2_riscv64.deb ... Unpacking python3 (3.10.1-0ubuntu2) ... Selecting previously unselected package libsigsegv2:riscv64. Preparing to unpack .../libsigsegv2_2.13-1ubuntu2_riscv64.deb ... Unpacking libsigsegv2:riscv64 (2.13-1ubuntu2) ... Setting up libsigsegv2:riscv64 (2.13-1ubuntu2) ... Selecting previously unselected package gawk. (Reading database ... 16053 files and directories currently installed.) Preparing to unpack .../000-gawk_1%3a5.1.0-1build2_riscv64.deb ... Unpacking gawk (1:5.1.0-1build2) ... Selecting previously unselected package sgml-base. Preparing to unpack .../001-sgml-base_1.30_all.deb ... Unpacking sgml-base (1.30) ... Selecting previously unselected package libmd0:riscv64. Preparing to unpack .../002-libmd0_1.0.4-1_riscv64.deb ... Unpacking libmd0:riscv64 (1.0.4-1) ... Selecting previously unselected package libbsd0:riscv64. Preparing to unpack .../003-libbsd0_0.11.5-1_riscv64.deb ... Unpacking libbsd0:riscv64 (0.11.5-1) ... Selecting previously unselected package libelf1:riscv64. Preparing to unpack .../004-libelf1_0.186-1_riscv64.deb ... Unpacking libelf1:riscv64 (0.186-1) ... Selecting previously unselected package libfribidi0:riscv64. Preparing to unpack .../005-libfribidi0_1.0.8-2ubuntu2_riscv64.deb ... Unpacking libfribidi0:riscv64 (1.0.8-2ubuntu2) ... Selecting previously unselected package libglib2.0-0:riscv64. Preparing to unpack .../006-libglib2.0-0_2.71.3-1_riscv64.deb ... Unpacking libglib2.0-0:riscv64 (2.71.3-1) ... Selecting previously unselected package libicu70:riscv64. Preparing to unpack .../007-libicu70_70.1-2_riscv64.deb ... Unpacking libicu70:riscv64 (70.1-2) ... Selecting previously unselected package libxml2:riscv64. Preparing to unpack .../008-libxml2_2.9.13+dfsg-1_riscv64.deb ... Unpacking libxml2:riscv64 (2.9.13+dfsg-1) ... Selecting previously unselected package libyaml-0-2:riscv64. Preparing to unpack .../009-libyaml-0-2_0.2.2-1build1_riscv64.deb ... Unpacking libyaml-0-2:riscv64 (0.2.2-1build1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../010-python3-pkg-resources_59.6.0-1.2_all.deb ... Unpacking python3-pkg-resources (59.6.0-1.2) ... Selecting previously unselected package ucf. Preparing to unpack .../011-ucf_3.0043_all.deb ... Moving old data out of the way Unpacking ucf (3.0043) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../012-bsdextrautils_2.37.2-4ubuntu3_riscv64.deb ... Unpacking bsdextrautils (2.37.2-4ubuntu3) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../013-libmagic-mgc_1%3a5.41-2_riscv64.deb ... Unpacking libmagic-mgc (1:5.41-2) ... Selecting previously unselected package libmagic1:riscv64. Preparing to unpack .../014-libmagic1_1%3a5.41-2_riscv64.deb ... Unpacking libmagic1:riscv64 (1:5.41-2) ... Selecting previously unselected package file. Preparing to unpack .../015-file_1%3a5.41-2_riscv64.deb ... Unpacking file (1:5.41-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../016-gettext-base_0.21-4ubuntu3_riscv64.deb ... Unpacking gettext-base (0.21-4ubuntu3) ... Selecting previously unselected package libuchardet0:riscv64. Preparing to unpack .../017-libuchardet0_0.0.7-1build1_riscv64.deb ... Unpacking libuchardet0:riscv64 (0.0.7-1build1) ... Selecting previously unselected package groff-base. Preparing to unpack .../018-groff-base_1.22.4-8_riscv64.deb ... Unpacking groff-base (1.22.4-8) ... Selecting previously unselected package libedit2:riscv64. Preparing to unpack .../019-libedit2_3.1-20210910-1_riscv64.deb ... Unpacking libedit2:riscv64 (3.1-20210910-1) ... Selecting previously unselected package libpipeline1:riscv64. Preparing to unpack .../020-libpipeline1_1.5.5-1_riscv64.deb ... Unpacking libpipeline1:riscv64 (1.5.5-1) ... Selecting previously unselected package libpsl5:riscv64. Preparing to unpack .../021-libpsl5_0.21.0-1.2build1_riscv64.deb ... Unpacking libpsl5:riscv64 (0.21.0-1.2build1) ... Selecting previously unselected package libxau6:riscv64. Preparing to unpack .../022-libxau6_1%3a1.0.9-1build4_riscv64.deb ... Unpacking libxau6:riscv64 (1:1.0.9-1build4) ... Selecting previously unselected package libxdmcp6:riscv64. Preparing to unpack .../023-libxdmcp6_1%3a1.1.3-0ubuntu4_riscv64.deb ... Unpacking libxdmcp6:riscv64 (1:1.1.3-0ubuntu4) ... Selecting previously unselected package libxcb1:riscv64. Preparing to unpack .../024-libxcb1_1.14-3ubuntu2_riscv64.deb ... Unpacking libxcb1:riscv64 (1.14-3ubuntu2) ... Selecting previously unselected package libx11-data. Preparing to unpack .../025-libx11-data_2%3a1.7.2-2_all.deb ... Unpacking libx11-data (2:1.7.2-2) ... Selecting previously unselected package libx11-6:riscv64. Preparing to unpack .../026-libx11-6_2%3a1.7.2-2_riscv64.deb ... Unpacking libx11-6:riscv64 (2:1.7.2-2) ... Selecting previously unselected package libxext6:riscv64. Preparing to unpack .../027-libxext6_2%3a1.3.4-1_riscv64.deb ... Unpacking libxext6:riscv64 (2:1.3.4-1) ... Selecting previously unselected package man-db. Preparing to unpack .../028-man-db_2.10.1-1_riscv64.deb ... Unpacking man-db (2.10.1-1) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../029-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package rake. Preparing to unpack .../030-rake_13.0.6-2_all.deb ... Unpacking rake (13.0.6-2) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../031-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../032-ruby-xmlrpc_0.3.2-1_all.deb ... Unpacking ruby-xmlrpc (0.3.2-1) ... Selecting previously unselected package libruby3.0:riscv64. Preparing to unpack .../033-libruby3.0_3.0.2-7ubuntu1_riscv64.deb ... Unpacking libruby3.0:riscv64 (3.0.2-7ubuntu1) ... Selecting previously unselected package ruby3.0. Preparing to unpack .../034-ruby3.0_3.0.2-7ubuntu1_riscv64.deb ... Unpacking ruby3.0 (3.0.2-7ubuntu1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../035-ruby-rubygems_3.3.5-2_all.deb ... Unpacking ruby-rubygems (3.3.5-2) ... Selecting previously unselected package ruby. Preparing to unpack .../036-ruby_1%3a3.0~exp1_riscv64.deb ... Unpacking ruby (1:3.0~exp1) ... Selecting previously unselected package ruby-asciidoctor. Preparing to unpack .../037-ruby-asciidoctor_2.0.16-2_all.deb ... Unpacking ruby-asciidoctor (2.0.16-2) ... Selecting previously unselected package asciidoctor. Preparing to unpack .../038-asciidoctor_2.0.16-2_all.deb ... Unpacking asciidoctor (2.0.16-2) ... Selecting previously unselected package m4. Preparing to unpack .../039-m4_1.4.18-5ubuntu1_riscv64.deb ... Unpacking m4 (1.4.18-5ubuntu1) ... Selecting previously unselected package autoconf. Preparing to unpack .../040-autoconf_2.71-2_all.deb ... Unpacking autoconf (2.71-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../041-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../042-automake_1%3a1.16.5-1.1ubuntu4_all.deb ... Unpacking automake (1:1.16.5-1.1ubuntu4) ... Selecting previously unselected package autopoint. Preparing to unpack .../043-autopoint_0.21-4ubuntu3_all.deb ... Unpacking autopoint (0.21-4ubuntu3) ... Selecting previously unselected package libtcl8.6:riscv64. Preparing to unpack .../044-libtcl8.6_8.6.12+dfsg-1_riscv64.deb ... Unpacking libtcl8.6:riscv64 (8.6.12+dfsg-1) ... Selecting previously unselected package libbrotli1:riscv64. Preparing to unpack .../045-libbrotli1_1.0.9-2build4_riscv64.deb ... Unpacking libbrotli1:riscv64 (1.0.9-2build4) ... Selecting previously unselected package libfreetype6:riscv64. Preparing to unpack .../046-libfreetype6_2.11.1+dfsg-1_riscv64.deb ... Unpacking libfreetype6:riscv64 (2.11.1+dfsg-1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../047-fonts-dejavu-core_2.37-2build1_all.deb ... Unpacking fonts-dejavu-core (2.37-2build1) ... Selecting previously unselected package fonts-urw-base35. Preparing to unpack .../048-fonts-urw-base35_20200910-1_all.deb ... Unpacking fonts-urw-base35 (20200910-1) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../049-fontconfig-config_2.13.1-4.2ubuntu4_all.deb ... Unpacking fontconfig-config (2.13.1-4.2ubuntu4) ... Selecting previously unselected package libfontconfig1:riscv64. Preparing to unpack .../050-libfontconfig1_2.13.1-4.2ubuntu4_riscv64.deb ... Unpacking libfontconfig1:riscv64 (2.13.1-4.2ubuntu4) ... Selecting previously unselected package libxrender1:riscv64. Preparing to unpack .../051-libxrender1_1%3a0.9.10-1build3_riscv64.deb ... Unpacking libxrender1:riscv64 (1:0.9.10-1build3) ... Selecting previously unselected package libxft2:riscv64. Preparing to unpack .../052-libxft2_2.3.3-0ubuntu4_riscv64.deb ... Unpacking libxft2:riscv64 (2.3.3-0ubuntu4) ... Selecting previously unselected package x11-common. Preparing to unpack .../053-x11-common_1%3a7.7+23ubuntu1_all.deb ... Unpacking x11-common (1:7.7+23ubuntu1) ... Selecting previously unselected package libxss1:riscv64. Preparing to unpack .../054-libxss1_1%3a1.2.3-1build1_riscv64.deb ... Unpacking libxss1:riscv64 (1:1.2.3-1build1) ... Selecting previously unselected package libtk8.6:riscv64. Preparing to unpack .../055-libtk8.6_8.6.12-1_riscv64.deb ... Unpacking libtk8.6:riscv64 (8.6.12-1) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../056-tk8.6-blt2.5_2.5.3+dfsg-4.1build1_riscv64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1build1) ... Selecting previously unselected package blt. Preparing to unpack .../057-blt_2.5.3+dfsg-4.1build1_riscv64.deb ... Unpacking blt (2.5.3+dfsg-4.1build1) ... Selecting previously unselected package cd-hit. Preparing to unpack .../058-cd-hit_4.8.1-4_riscv64.deb ... Unpacking cd-hit (4.8.1-4) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../059-libdebhelper-perl_13.6ubuntu1_all.deb ... Unpacking libdebhelper-perl (13.6ubuntu1) ... Selecting previously unselected package libtool. Preparing to unpack .../060-libtool_2.4.6-15build1_all.deb ... Unpacking libtool (2.4.6-15build1) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../061-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../062-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../063-libsub-override-perl_0.09-2_all.deb ... Unpacking libsub-override-perl (0.09-2) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../064-libfile-stripnondeterminism-perl_1.13.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../065-dh-strip-nondeterminism_1.13.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.0-1) ... Selecting previously unselected package libdw1:riscv64. Preparing to unpack .../066-libdw1_0.186-1_riscv64.deb ... Unpacking libdw1:riscv64 (0.186-1) ... Selecting previously unselected package debugedit. Preparing to unpack .../067-debugedit_1%3a5.0-4_riscv64.deb ... Unpacking debugedit (1:5.0-4) ... Selecting previously unselected package dwz. Preparing to unpack .../068-dwz_0.14-1build1_riscv64.deb ... Unpacking dwz (0.14-1build1) ... Selecting previously unselected package gettext. Preparing to unpack .../069-gettext_0.21-4ubuntu3_riscv64.deb ... Unpacking gettext (0.21-4ubuntu3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../070-intltool-debian_0.35.0+20060710.5_all.deb ... Unpacking intltool-debian (0.35.0+20060710.5) ... Selecting previously unselected package po-debconf. Preparing to unpack .../071-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../072-debhelper_13.6ubuntu1_all.deb ... Unpacking debhelper (13.6ubuntu1) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../073-python3-lib2to3_3.10.3-0ubuntu2_all.deb ... Unpacking python3-lib2to3 (3.10.3-0ubuntu2) ... Selecting previously unselected package python3-distutils. Preparing to unpack .../074-python3-distutils_3.10.3-0ubuntu2_all.deb ... Unpacking python3-distutils (3.10.3-0ubuntu2) ... Selecting previously unselected package dh-python. Preparing to unpack .../075-dh-python_5.20220215_all.deb ... Unpacking dh-python (5.20220215) ... Selecting previously unselected package libsasl2-modules-db:riscv64. Preparing to unpack .../076-libsasl2-modules-db_2.1.27+dfsg2-3ubuntu1_riscv64.deb ... Unpacking libsasl2-modules-db:riscv64 (2.1.27+dfsg2-3ubuntu1) ... Selecting previously unselected package libsasl2-2:riscv64. Preparing to unpack .../077-libsasl2-2_2.1.27+dfsg2-3ubuntu1_riscv64.deb ... Unpacking libsasl2-2:riscv64 (2.1.27+dfsg2-3ubuntu1) ... Selecting previously unselected package libldap-2.5-0:riscv64. Preparing to unpack .../078-libldap-2.5-0_2.5.11+dfsg-1~exp1ubuntu3_riscv64.deb ... Unpacking libldap-2.5-0:riscv64 (2.5.11+dfsg-1~exp1ubuntu3) ... Selecting previously unselected package libnghttp2-14:riscv64. Preparing to unpack .../079-libnghttp2-14_1.43.0-1build2_riscv64.deb ... Unpacking libnghttp2-14:riscv64 (1.43.0-1build2) ... Selecting previously unselected package librtmp1:riscv64. Preparing to unpack .../080-librtmp1_2.4+20151223.gitfa8646d.1-2build3_riscv64.deb ... Unpacking librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build3) ... Selecting previously unselected package libssh-4:riscv64. Preparing to unpack .../081-libssh-4_0.9.6-2_riscv64.deb ... Unpacking libssh-4:riscv64 (0.9.6-2) ... Selecting previously unselected package libcurl3-gnutls:riscv64. Preparing to unpack .../082-libcurl3-gnutls_7.81.0-1_riscv64.deb ... Unpacking libcurl3-gnutls:riscv64 (7.81.0-1) ... Selecting previously unselected package libdeflate0:riscv64. Preparing to unpack .../083-libdeflate0_1.10-1ubuntu1_riscv64.deb ... Unpacking libdeflate0:riscv64 (1.10-1ubuntu1) ... Selecting previously unselected package libhtscodecs2:riscv64. Preparing to unpack .../084-libhtscodecs2_1.1.1-3_riscv64.deb ... Unpacking libhtscodecs2:riscv64 (1.1.1-3) ... Selecting previously unselected package libhts3:riscv64. Preparing to unpack .../085-libhts3_1.13+ds-2build1_riscv64.deb ... Unpacking libhts3:riscv64 (1.13+ds-2build1) ... Selecting previously unselected package samtools. Preparing to unpack .../086-samtools_1.13-4_riscv64.deb ... Unpacking samtools (1.13-4) ... Selecting previously unselected package fastaq. Preparing to unpack .../087-fastaq_3.17.0-4_all.deb ... Unpacking fastaq (3.17.0-4) ... Selecting previously unselected package fonts-lyx. Preparing to unpack .../088-fonts-lyx_2.3.6-1_all.deb ... Unpacking fonts-lyx (2.3.6-1) ... Selecting previously unselected package help2man. Preparing to unpack .../089-help2man_1.49.1_riscv64.deb ... Unpacking help2man (1.49.1) ... Selecting previously unselected package libblas3:riscv64. Preparing to unpack .../090-libblas3_3.10.0-2ubuntu1_riscv64.deb ... Unpacking libblas3:riscv64 (3.10.0-2ubuntu1) ... Selecting previously unselected package libcapnp-0.8.0:riscv64. Preparing to unpack .../091-libcapnp-0.8.0_0.8.0-2ubuntu2_riscv64.deb ... Unpacking libcapnp-0.8.0:riscv64 (0.8.0-2ubuntu2) ... Selecting previously unselected package libexpat1-dev:riscv64. Preparing to unpack .../092-libexpat1-dev_2.4.7-1_riscv64.deb ... Unpacking libexpat1-dev:riscv64 (2.4.7-1) ... Selecting previously unselected package libfml0:riscv64. Preparing to unpack .../093-libfml0_0.1+git20190320.b499514-1_riscv64.deb ... Unpacking libfml0:riscv64 (0.1+git20190320.b499514-1) ... Selecting previously unselected package zlib1g-dev:riscv64. Preparing to unpack .../094-zlib1g-dev_1%3a1.2.11.dfsg-2ubuntu8_riscv64.deb ... Unpacking zlib1g-dev:riscv64 (1:1.2.11.dfsg-2ubuntu8) ... Selecting previously unselected package libfml-dev:riscv64. Preparing to unpack .../095-libfml-dev_0.1+git20190320.b499514-1_riscv64.deb ... Unpacking libfml-dev:riscv64 (0.1+git20190320.b499514-1) ... Selecting previously unselected package libgfortran5:riscv64. Preparing to unpack .../096-libgfortran5_12-20220313-1ubuntu1_riscv64.deb ... Unpacking libgfortran5:riscv64 (12-20220313-1ubuntu1) ... Selecting previously unselected package libgraphite2-3:riscv64. Preparing to unpack .../097-libgraphite2-3_1.3.14-1build1_riscv64.deb ... Unpacking libgraphite2-3:riscv64 (1.3.14-1build1) ... Selecting previously unselected package libgslcblas0:riscv64. Preparing to unpack .../098-libgslcblas0_2.7.1+dfsg-3_riscv64.deb ... Unpacking libgslcblas0:riscv64 (2.7.1+dfsg-3) ... Selecting previously unselected package libgsl27:riscv64. Preparing to unpack .../099-libgsl27_2.7.1+dfsg-3_riscv64.deb ... Unpacking libgsl27:riscv64 (2.7.1+dfsg-3) ... Selecting previously unselected package libharfbuzz0b:riscv64. Preparing to unpack .../100-libharfbuzz0b_2.7.4-1ubuntu3_riscv64.deb ... Unpacking libharfbuzz0b:riscv64 (2.7.4-1ubuntu3) ... Selecting previously unselected package libimagequant0:riscv64. Preparing to unpack .../101-libimagequant0_2.17.0-1_riscv64.deb ... Unpacking libimagequant0:riscv64 (2.17.0-1) ... Selecting previously unselected package libjpeg-turbo8:riscv64. Preparing to unpack .../102-libjpeg-turbo8_2.1.2-0ubuntu1_riscv64.deb ... Unpacking libjpeg-turbo8:riscv64 (2.1.2-0ubuntu1) ... Selecting previously unselected package libjpeg8:riscv64. Preparing to unpack .../103-libjpeg8_8c-2ubuntu8_riscv64.deb ... Unpacking libjpeg8:riscv64 (8c-2ubuntu8) ... Selecting previously unselected package libjs-jquery. Preparing to unpack .../104-libjs-jquery_3.6.0+dfsg+~3.5.13-1_all.deb ... Unpacking libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Selecting previously unselected package libjs-jquery-ui. Preparing to unpack .../105-libjs-jquery-ui_1.13.1+dfsg-1_all.deb ... Unpacking libjs-jquery-ui (1.13.1+dfsg-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../106-libjs-underscore_1.13.2~dfsg-2_all.deb ... Unpacking libjs-underscore (1.13.2~dfsg-2) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../107-libjs-sphinxdoc_4.3.2-1_all.deb ... Unpacking libjs-sphinxdoc (4.3.2-1) ... Selecting previously unselected package liblapack3:riscv64. Preparing to unpack .../108-liblapack3_3.10.0-2ubuntu1_riscv64.deb ... Unpacking liblapack3:riscv64 (3.10.0-2ubuntu1) ... Selecting previously unselected package liblbfgsb0:riscv64. Preparing to unpack .../109-liblbfgsb0_3.0+dfsg.3-10_riscv64.deb ... Unpacking liblbfgsb0:riscv64 (3.0+dfsg.3-10) ... Selecting previously unselected package liblcms2-2:riscv64. Preparing to unpack .../110-liblcms2-2_2.12~rc1-2build1_riscv64.deb ... Unpacking liblcms2-2:riscv64 (2.12~rc1-2build1) ... Selecting previously unselected package libminimap0:riscv64. Preparing to unpack .../111-libminimap0_0.2-6_riscv64.deb ... Unpacking libminimap0:riscv64 (0.2-6) ... Selecting previously unselected package libminimap-dev:riscv64. Preparing to unpack .../112-libminimap-dev_0.2-6_riscv64.deb ... Unpacking libminimap-dev:riscv64 (0.2-6) ... Selecting previously unselected package libmurmurhash2:riscv64. Preparing to unpack .../113-libmurmurhash2_1.5-3_riscv64.deb ... Unpacking libmurmurhash2:riscv64 (1.5-3) ... Selecting previously unselected package libpython3.10:riscv64. Preparing to unpack .../114-libpython3.10_3.10.3-1_riscv64.deb ... Unpacking libpython3.10:riscv64 (3.10.3-1) ... Selecting previously unselected package libpython3.10-dev:riscv64. Preparing to unpack .../115-libpython3.10-dev_3.10.3-1_riscv64.deb ... Unpacking libpython3.10-dev:riscv64 (3.10.3-1) ... Selecting previously unselected package libpython3-dev:riscv64. Preparing to unpack .../116-libpython3-dev_3.10.1-0ubuntu2_riscv64.deb ... Unpacking libpython3-dev:riscv64 (3.10.1-0ubuntu2) ... Selecting previously unselected package libpython3-all-dev:riscv64. Preparing to unpack .../117-libpython3-all-dev_3.10.1-0ubuntu2_riscv64.deb ... Unpacking libpython3-all-dev:riscv64 (3.10.1-0ubuntu2) ... Selecting previously unselected package libqhull-r8.0:riscv64. Preparing to unpack .../118-libqhull-r8.0_2020.2-4_riscv64.deb ... Unpacking libqhull-r8.0:riscv64 (2020.2-4) ... Selecting previously unselected package libraqm0:riscv64. Preparing to unpack .../119-libraqm0_0.7.0-4ubuntu1_riscv64.deb ... Unpacking libraqm0:riscv64 (0.7.0-4ubuntu1) ... Selecting previously unselected package libjbig0:riscv64. Preparing to unpack .../120-libjbig0_2.1-3.1build2_riscv64.deb ... Unpacking libjbig0:riscv64 (2.1-3.1build2) ... Selecting previously unselected package libwebp7:riscv64. Preparing to unpack .../121-libwebp7_1.2.2-2_riscv64.deb ... Unpacking libwebp7:riscv64 (1.2.2-2) ... Selecting previously unselected package libtiff5:riscv64. Preparing to unpack .../122-libtiff5_4.3.0-6_riscv64.deb ... Unpacking libtiff5:riscv64 (4.3.0-6) ... Selecting previously unselected package libwebpdemux2:riscv64. Preparing to unpack .../123-libwebpdemux2_1.2.2-2_riscv64.deb ... Unpacking libwebpdemux2:riscv64 (1.2.2-2) ... Selecting previously unselected package libwebpmux3:riscv64. Preparing to unpack .../124-libwebpmux3_1.2.2-2_riscv64.deb ... Unpacking libwebpmux3:riscv64 (1.2.2-2) ... Selecting previously unselected package libxslt1.1:riscv64. Preparing to unpack .../125-libxslt1.1_1.1.34-4build1_riscv64.deb ... Unpacking libxslt1.1:riscv64 (1.1.34-4build1) ... Selecting previously unselected package mash. Preparing to unpack .../126-mash_2.3+dfsg-1build2_riscv64.deb ... Unpacking mash (2.3+dfsg-1build2) ... Selecting previously unselected package mummer. Preparing to unpack .../127-mummer_3.23+dfsg-7_riscv64.deb ... Unpacking mummer (3.23+dfsg-7) ... Selecting previously unselected package python-matplotlib-data. Preparing to unpack .../128-python-matplotlib-data_3.5.1-2build1_all.deb ... Unpacking python-matplotlib-data (3.5.1-2build1) ... Selecting previously unselected package python3-all. Preparing to unpack .../129-python3-all_3.10.1-0ubuntu2_riscv64.deb ... Unpacking python3-all (3.10.1-0ubuntu2) ... Selecting previously unselected package python3.10-dev. Preparing to unpack .../130-python3.10-dev_3.10.3-1_riscv64.deb ... Unpacking python3.10-dev (3.10.3-1) ... Selecting previously unselected package python3-dev. Preparing to unpack .../131-python3-dev_3.10.1-0ubuntu2_riscv64.deb ... Unpacking python3-dev (3.10.1-0ubuntu2) ... Selecting previously unselected package python3-all-dev. Preparing to unpack .../132-python3-all-dev_3.10.1-0ubuntu2_riscv64.deb ... Unpacking python3-all-dev (3.10.1-0ubuntu2) ... Selecting previously unselected package python3-appdirs. Preparing to unpack .../133-python3-appdirs_1.4.4-2_all.deb ... Unpacking python3-appdirs (1.4.4-2) ... Selecting previously unselected package python3-attr. Preparing to unpack .../134-python3-attr_21.2.0-1_all.deb ... Unpacking python3-attr (21.2.0-1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../135-python3-numpy_1%3a1.21.5-1build1_riscv64.deb ... Unpacking python3-numpy (1:1.21.5-1build1) ... Selecting previously unselected package python3-renderpm:riscv64. Preparing to unpack .../136-python3-renderpm_3.6.8-1_riscv64.deb ... Unpacking python3-renderpm:riscv64 (3.6.8-1) ... Selecting previously unselected package python3-reportlab-accel:riscv64. Preparing to unpack .../137-python3-reportlab-accel_3.6.8-1_riscv64.deb ... Unpacking python3-reportlab-accel:riscv64 (3.6.8-1) ... Selecting previously unselected package python3-tk:riscv64. Preparing to unpack .../138-python3-tk_3.10.3-0ubuntu2_riscv64.deb ... Unpacking python3-tk:riscv64 (3.10.3-0ubuntu2) ... Selecting previously unselected package python3-pil.imagetk:riscv64. Preparing to unpack .../139-python3-pil.imagetk_9.0.1-1_riscv64.deb ... Unpacking python3-pil.imagetk:riscv64 (9.0.1-1) ... Selecting previously unselected package libopenjp2-7:riscv64. Preparing to unpack .../140-libopenjp2-7_2.4.0-6_riscv64.deb ... Unpacking libopenjp2-7:riscv64 (2.4.0-6) ... Selecting previously unselected package python3-pil:riscv64. Preparing to unpack .../141-python3-pil_9.0.1-1_riscv64.deb ... Unpacking python3-pil:riscv64 (9.0.1-1) ... Selecting previously unselected package python3-reportlab. Preparing to unpack .../142-python3-reportlab_3.6.8-1_all.deb ... Unpacking python3-reportlab (3.6.8-1) ... Selecting previously unselected package xml-core. Preparing to unpack .../143-xml-core_0.18+nmu1_all.deb ... Unpacking xml-core (0.18+nmu1) ... Selecting previously unselected package w3-dtd-mathml. Preparing to unpack .../144-w3-dtd-mathml_2.0.0.0-5.1_all.deb ... Unpacking w3-dtd-mathml (2.0.0.0-5.1) ... Selecting previously unselected package python3-biopython. Preparing to unpack .../145-python3-biopython_1.79+dfsg-2_riscv64.deb ... Unpacking python3-biopython (1.79+dfsg-2) ... Selecting previously unselected package python3-brotli. Preparing to unpack .../146-python3-brotli_1.0.9-2build4_riscv64.deb ... Unpacking python3-brotli (1.0.9-2build4) ... Selecting previously unselected package python3-soupsieve. Preparing to unpack .../147-python3-soupsieve_2.3.1-1_all.deb ... Unpacking python3-soupsieve (2.3.1-1) ... Selecting previously unselected package python3-bs4. Preparing to unpack .../148-python3-bs4_4.10.0-2_all.deb ... Unpacking python3-bs4 (4.10.0-2) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../149-python3-cycler_0.11.0-1_all.deb ... Unpacking python3-cycler (0.11.0-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../150-python3-six_1.16.0-3_all.deb ... Unpacking python3-six (1.16.0-3) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../151-python3-dateutil_2.8.1-6_all.deb ... Unpacking python3-dateutil (2.8.1-6) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../152-python3-decorator_4.4.2-0ubuntu1_all.deb ... Unpacking python3-decorator (4.4.2-0ubuntu1) ... Selecting previously unselected package python3-dendropy. Preparing to unpack .../153-python3-dendropy_4.5.2-1_all.deb ... Unpacking python3-dendropy (4.5.2-1) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../154-python3-scipy_1.8.0-1exp2build1_riscv64.deb ... Unpacking python3-scipy (1.8.0-1exp2build1) ... Selecting previously unselected package python3-ufolib2. Preparing to unpack .../155-python3-ufolib2_0.13.1+dfsg1-1_all.deb ... Unpacking python3-ufolib2 (0.13.1+dfsg1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../156-python3-mpmath_1.2.1-2_all.deb ... Unpacking python3-mpmath (1.2.1-2) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../157-python3-sympy_1.9-1_all.deb ... Unpacking python3-sympy (1.9-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../158-python3-tz_2021.3-1_all.deb ... Unpacking python3-tz (2021.3-1) ... Selecting previously unselected package python3-fs. Preparing to unpack .../159-python3-fs_2.4.12-1_all.deb ... Unpacking python3-fs (2.4.12-1) ... Selecting previously unselected package python3-lxml:riscv64. Preparing to unpack .../160-python3-lxml_4.8.0-1build1_riscv64.deb ... Unpacking python3-lxml:riscv64 (4.8.0-1build1) ... Selecting previously unselected package python3-lz4. Preparing to unpack .../161-python3-lz4_3.1.3+dfsg-1build2_riscv64.deb ... Unpacking python3-lz4 (3.1.3+dfsg-1build2) ... Selecting previously unselected package python3-unicodedata2. Preparing to unpack .../162-python3-unicodedata2_14.0.0+ds-8_riscv64.deb ... Unpacking python3-unicodedata2 (14.0.0+ds-8) ... Selecting previously unselected package unicode-data. Preparing to unpack .../163-unicode-data_14.0.0-1.1_all.deb ... Unpacking unicode-data (14.0.0-1.1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../164-python3-fonttools_4.29.1-2build1_riscv64.deb ... Unpacking python3-fonttools (4.29.1-2build1) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../165-python3-more-itertools_8.10.0-2_all.deb ... Unpacking python3-more-itertools (8.10.0-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../166-python3-zipp_1.0.0-3_all.deb ... Unpacking python3-zipp (1.0.0-3) ... Selecting previously unselected package python3-importlib-metadata. Preparing to unpack .../167-python3-importlib-metadata_4.6.4-1_all.deb ... Unpacking python3-importlib-metadata (4.6.4-1) ... Selecting previously unselected package python3-iniconfig. Preparing to unpack .../168-python3-iniconfig_1.1.1-2_all.deb ... Unpacking python3-iniconfig (1.1.1-2) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../169-python3-kiwisolver_1.3.2-1_riscv64.deb ... Unpacking python3-kiwisolver (1.3.2-1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../170-python3-pyparsing_2.4.7-1_all.deb ... Unpacking python3-pyparsing (2.4.7-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../171-python3-packaging_21.3-1_all.deb ... Unpacking python3-packaging (21.3-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../172-python3-matplotlib_3.5.1-2build1_riscv64.deb ... Unpacking python3-matplotlib (3.5.1-2build1) ... Selecting previously unselected package python3-pluggy. Preparing to unpack .../173-python3-pluggy_0.13.0-7.1_all.deb ... Unpacking python3-pluggy (0.13.0-7.1) ... Selecting previously unselected package python3-py. Preparing to unpack .../174-python3-py_1.10.0-1_all.deb ... Unpacking python3-py (1.10.0-1) ... Selecting previously unselected package python3-pymummer. Preparing to unpack .../175-python3-pymummer_0.11.0-2_all.deb ... Unpacking python3-pymummer (0.11.0-2) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../176-python3-pysam_0.17.0+ds-2build1_riscv64.deb ... Unpacking python3-pysam (0.17.0+ds-2build1) ... Selecting previously unselected package python3-toml. Preparing to unpack .../177-python3-toml_0.10.2-1_all.deb ... Unpacking python3-toml (0.10.2-1) ... Selecting previously unselected package python3-pytest. Preparing to unpack .../178-python3-pytest_6.2.5-1ubuntu2_all.deb ... Unpacking python3-pytest (6.2.5-1ubuntu2) ... Selecting previously unselected package python3-setuptools. Preparing to unpack .../179-python3-setuptools_59.6.0-1.2_all.deb ... Unpacking python3-setuptools (59.6.0-1.2) ... Selecting previously unselected package bowtie2. Preparing to unpack .../180-bowtie2_2.4.5-1_riscv64.deb ... Unpacking bowtie2 (2.4.5-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../181-sbuild-build-depends-main-dummy_0.invalid.0_riscv64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up cd-hit (4.8.1-4) ... Setting up libhtscodecs2:riscv64 (1.1.1-3) ... Setting up media-types (6.0.0) ... Setting up libpipeline1:riscv64 (1.5.5-1) ... Setting up libgraphite2-3:riscv64 (1.3.14-1build1) ... Setting up liblcms2-2:riscv64 (2.12~rc1-2build1) ... Setting up libxau6:riscv64 (1:1.0.9-1build4) ... Setting up libpsl5:riscv64 (0.21.0-1.2build1) ... Setting up bsdextrautils (2.37.2-4ubuntu3) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libgslcblas0:riscv64 (2.7.1+dfsg-3) ... Setting up libmurmurhash2:riscv64 (1.5-3) ... Setting up libmagic-mgc (1:5.41-2) ... Setting up gawk (1:5.1.0-1build2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:riscv64 (0.2.2-1build1) ... Setting up libglib2.0-0:riscv64 (2.71.3-1) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.6-1) ... Setting up libdebhelper-perl (13.6ubuntu1) ... Setting up libbrotli1:riscv64 (1.0.9-2build4) ... Setting up libcapnp-0.8.0:riscv64 (0.8.0-2ubuntu2) ... Setting up x11-common (1:7.7+23ubuntu1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:riscv64 (1.43.0-1build2) ... Setting up libmagic1:riscv64 (1:5.41-2) ... Setting up libdeflate0:riscv64 (1.10-1ubuntu1) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up libgsl27:riscv64 (2.7.1+dfsg-3) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libqhull-r8.0:riscv64 (2020.2-4) ... Setting up rubygems-integration (1.18) ... Setting up file (1:5.41-2) ... Setting up fonts-urw-base35 (20200910-1) ... Setting up libfml0:riscv64 (0.1+git20190320.b499514-1) ... Setting up libjbig0:riscv64 (2.1-3.1build2) ... Setting up libsasl2-modules-db:riscv64 (2.1.27+dfsg2-3ubuntu1) ... Setting up unicode-data (14.0.0-1.1) ... Setting up libminimap0:riscv64 (0.2-6) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:riscv64 (3.10.0-2ubuntu1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/riscv64-linux-gnu/libblas.so.3 (libblas.so.3-riscv64-linux-gnu) in auto mode Setting up libexpat1-dev:riscv64 (2.4.7-1) ... Setting up libfreetype6:riscv64 (2.11.1+dfsg-1) ... Setting up libx11-data (2:1.7.2-2) ... Setting up librtmp1:riscv64 (2.4+20151223.gitfa8646d.1-2build3) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libfribidi0:riscv64 (1.0.8-2ubuntu2) ... Setting up libimagequant0:riscv64 (2.17.0-1) ... Setting up mash (2.3+dfsg-1build2) ... Setting up libtcl8.6:riscv64 (8.6.12+dfsg-1) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up fonts-dejavu-core (2.37-2build1) ... Setting up ucf (3.0043) ... Setting up libjpeg-turbo8:riscv64 (2.1.2-0ubuntu1) ... Setting up libsasl2-2:riscv64 (2.1.27+dfsg2-3ubuntu1) ... Setting up libssh-4:riscv64 (0.9.6-2) ... Setting up libgfortran5:riscv64 (12-20220313-1ubuntu1) ... Setting up autoconf (2.71-2) ... Setting up libwebp7:riscv64 (1.2.2-2) ... Setting up zlib1g-dev:riscv64 (1:1.2.11.dfsg-2ubuntu8) ... Setting up libmd0:riscv64 (1.0.4-1) ... Setting up libuchardet0:riscv64 (0.0.7-1build1) ... Setting up libmpdec3:riscv64 (2.5.1-2build1) ... Setting up mummer (3.23+dfsg-7) ... Setting up libopenjp2-7:riscv64 (2.4.0-6) ... Setting up libsub-override-perl (0.09-2) ... Setting up libharfbuzz0b:riscv64 (2.7.4-1ubuntu3) ... Setting up sgml-base (1.30) ... Setting up libjs-jquery (3.6.0+dfsg+~3.5.13-1) ... Setting up python-matplotlib-data (3.5.1-2build1) ... Setting up libwebpmux3:riscv64 (1.2.2-2) ... Setting up libbsd0:riscv64 (0.11.5-1) ... Setting up mailcap (3.70+nmu1ubuntu1) ... Setting up libelf1:riscv64 (0.186-1) ... Setting up ruby-xmlrpc (0.3.2-1) ... Setting up liblocale-gettext-perl (1.07-4build3) ... Setting up libjs-underscore (1.13.2~dfsg-2) ... Setting up libicu70:riscv64 (70.1-2) ... Setting up libjpeg8:riscv64 (8c-2ubuntu8) ... Setting up automake (1:1.16.5-1.1ubuntu4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.0-1) ... Setting up libdw1:riscv64 (0.186-1) ... Setting up libxdmcp6:riscv64 (1:1.1.3-0ubuntu4) ... Setting up liblapack3:riscv64 (3.10.0-2ubuntu1) ... update-alternatives: using /usr/lib/riscv64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/riscv64-linux-gnu/liblapack.so.3 (liblapack.so.3-riscv64-linux-gnu) in auto mode Setting up libxcb1:riscv64 (1.14-3ubuntu2) ... Setting up libfml-dev:riscv64 (0.1+git20190320.b499514-1) ... Setting up mime-support (3.66) ... Setting up libtool (2.4.6-15build1) ... Setting up fontconfig-config (2.13.1-4.2ubuntu4) ... Setting up libwebpdemux2:riscv64 (1.2.2-2) ... Setting up libedit2:riscv64 (3.1-20210910-1) ... Setting up libldap-2.5-0:riscv64 (2.5.11+dfsg-1~exp1ubuntu3) ... Setting up help2man (1.49.1) ... Setting up libpython3.10-stdlib:riscv64 (3.10.3-1) ... Setting up dh-autoreconf (20) ... Setting up libjs-jquery-ui (1.13.1+dfsg-1) ... Setting up libraqm0:riscv64 (0.7.0-4ubuntu1) ... Setting up libminimap-dev:riscv64 (0.2-6) ... Setting up libjs-sphinxdoc (4.3.2-1) ... Setting up dh-strip-nondeterminism (1.13.0-1) ... Setting up dwz (0.14-1build1) ... Setting up groff-base (1.22.4-8) ... Setting up xml-core (0.18+nmu1) ... Setting up debugedit (1:5.0-4) ... Setting up libx11-6:riscv64 (2:1.7.2-2) ... Setting up libtiff5:riscv64 (4.3.0-6) ... Setting up libfontconfig1:riscv64 (2.13.1-4.2ubuntu4) ... Setting up libxml2:riscv64 (2.9.13+dfsg-1) ... Setting up libpython3-stdlib:riscv64 (3.10.1-0ubuntu2) ... Setting up liblbfgsb0:riscv64 (3.0+dfsg.3-10) ... Setting up libpython3.10:riscv64 (3.10.3-1) ... Setting up gettext (0.21-4ubuntu3) ... Setting up python3.10 (3.10.3-1) ... Setting up libxrender1:riscv64 (1:0.9.10-1build3) ... Setting up libxext6:riscv64 (2:1.3.4-1) ... Setting up libcurl3-gnutls:riscv64 (7.81.0-1) ... Setting up python3 (3.10.1-0ubuntu2) ... Setting up man-db (2.10.1-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up python3-tz (2021.3-1) ... Setting up bowtie2 (2.4.5-1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.16.0-3) ... Setting up python3-pil:riscv64 (9.0.1-1) ... Setting up python3-decorator (4.4.2-0ubuntu1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-brotli (1.0.9-2build4) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-reportlab-accel:riscv64 (3.6.8-1) ... Setting up python3-kiwisolver (1.3.2-1) ... Setting up libpython3.10-dev:riscv64 (3.10.3-1) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-reportlab (3.6.8-1) ... Setting up python3.10-dev (3.10.3-1) ... Setting up libxslt1.1:riscv64 (1.1.34-4build1) ... Setting up python3-dateutil (2.8.1-6) ... Setting up libxss1:riscv64 (1:1.2.3-1build1) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.10.3-0ubuntu2) ... Setting up python3-appdirs (1.4.4-2) ... Setting up python3-soupsieve (2.3.1-1) ... Setting up python3-pkg-resources (59.6.0-1.2) ... Setting up python3-distutils (3.10.3-0ubuntu2) ... Setting up dh-python (5.20220215) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-iniconfig (1.1.1-2) ... Setting up python3-sympy (1.9-1) ... Setting up python3-attr (21.2.0-1) ... Setting up libxft2:riscv64 (2.3.3-0ubuntu4) ... Setting up libhts3:riscv64 (1.13+ds-2build1) ... Setting up python3-pysam (0.17.0+ds-2build1) ... Setting up libpython3-dev:riscv64 (3.10.1-0ubuntu2) ... Setting up python3-renderpm:riscv64 (3.6.8-1) ... Setting up python3-setuptools (59.6.0-1.2) ... Setting up python3-py (1.10.0-1) ... Setting up python3-lz4 (3.1.3+dfsg-1build2) ... Setting up python3-unicodedata2 (14.0.0+ds-8) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:riscv64 (8.6.12-1) ... Setting up python3-all (3.10.1-0ubuntu2) ... Setting up debhelper (13.6ubuntu1) ... Setting up python3-zipp (1.0.0-3) ... Setting up python3-bs4 (4.10.0-2) ... Setting up samtools (1.13-4) ... Setting up python3-fs (2.4.12-1) ... Setting up python3-packaging (21.3-1) ... Setting up libpython3-all-dev:riscv64 (3.10.1-0ubuntu2) ... Setting up python3-dev (3.10.1-0ubuntu2) ... Setting up python3-numpy (1:1.21.5-1build1) ... Setting up python3-lxml:riscv64 (4.8.0-1build1) ... Setting up python3-dendropy (4.5.2-1) ... Setting up python3-all-dev (3.10.1-0ubuntu2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1build1) ... Setting up python3-scipy (1.8.0-1exp2build1) ... Setting up python3-importlib-metadata (4.6.4-1) ... Setting up blt (2.5.3+dfsg-4.1build1) ... Setting up fastaq (3.17.0-4) ... Setting up python3-tk:riscv64 (3.10.3-0ubuntu2) ... Setting up python3-pymummer (0.11.0-2) ... Setting up python3-pil.imagetk:riscv64 (9.0.1-1) ... Setting up python3-pluggy (0.13.0-7.1) ... Setting up python3-pytest (6.2.5-1ubuntu2) ... Setting up rake (13.0.6-2) ... Setting up python3-ufolib2 (0.13.1+dfsg1-1) ... Setting up libruby3.0:riscv64 (3.0.2-7ubuntu1) ... Setting up ruby-rubygems (3.3.5-2) ... Setting up python3-fonttools (4.29.1-2build1) ... Setting up ruby3.0 (3.0.2-7ubuntu1) ... Setting up python3-matplotlib (3.5.1-2build1) ... Setting up ruby (1:3.0~exp1) ... Setting up ruby-asciidoctor (2.0.16-2) ... Setting up asciidoctor (2.0.16-2) ... Processing triggers for libc-bin (2.35-0ubuntu3) ... Processing triggers for sgml-base (1.30) ... Setting up w3-dtd-mathml (2.0.0.0-5.1) ... Processing triggers for sgml-base (1.30) ... Setting up python3-biopython (1.79+dfsg-2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.11.0-1029-generic #32~20.04.1-Ubuntu SMP Fri Jan 28 13:38:22 UTC 2022 riscv64 (riscv64) Toolchain package versions: binutils_2.38-3ubuntu1 dpkg-dev_1.21.1ubuntu1 g++-11_11.2.0-18ubuntu1 gcc-11_11.2.0-18ubuntu1 libc6-dev_2.35-0ubuntu3 libstdc++-11-dev_11.2.0-18ubuntu1 libstdc++6_12-20220313-1ubuntu1 linux-libc-dev_5.15.0-23.23 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.4.1 asciidoctor_2.0.16-2 autoconf_2.71-2 automake_1:1.16.5-1.1ubuntu4 autopoint_0.21-4ubuntu3 autotools-dev_20220109.1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-6ubuntu1 binutils_2.38-3ubuntu1 binutils-common_2.38-3ubuntu1 binutils-riscv64-linux-gnu_2.38-3ubuntu1 blt_2.5.3+dfsg-4.1build1 bowtie2_2.4.5-1 bsdextrautils_2.37.2-4ubuntu3 bsdutils_1:2.37.2-4ubuntu3 build-essential_12.9ubuntu2 bzip2_1.0.8-5 ca-certificates_20211016 cd-hit_4.8.1-4 coreutils_8.32-4.1ubuntu1 cpp_4:11.2.0-1ubuntu1 cpp-11_11.2.0-18ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79ubuntu1 debhelper_13.6ubuntu1 debianutils_5.5-1ubuntu1 debugedit_1:5.0-4 dh-autoreconf_20 dh-python_5.20220215 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-0ubuntu1 dpkg_1.21.1ubuntu1 dpkg-dev_1.21.1ubuntu1 dwz_0.14-1build1 e2fsprogs_1.46.5-2ubuntu1 fakeroot_1.28-1ubuntu1 fastaq_3.17.0-4 file_1:5.41-2 findutils_4.8.0-1ubuntu2 fontconfig-config_2.13.1-4.2ubuntu4 fonts-dejavu-core_2.37-2build1 fonts-lyx_2.3.6-1 fonts-urw-base35_20200910-1 g++_4:11.2.0-1ubuntu1 g++-11_11.2.0-18ubuntu1 gawk_1:5.1.0-1build2 gcc_4:11.2.0-1ubuntu1 gcc-11_11.2.0-18ubuntu1 gcc-11-base_11.2.0-18ubuntu1 gcc-12-base_12-20220313-1ubuntu1 gettext_0.21-4ubuntu3 gettext-base_0.21-4ubuntu3 gpg_2.2.27-3ubuntu1 gpg-agent_2.2.27-3ubuntu1 gpgconf_2.2.27-3ubuntu1 gpgv_2.2.27-3ubuntu1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.10-4ubuntu2 help2man_1.49.1 hostname_3.23ubuntu1 init_1.62 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapparmor1_3.0.4-2ubuntu2 libapt-pkg6.0_2.4.1 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.3 libasan6_11.2.0-18ubuntu1 libassuan0_2.5.5-1 libatomic1_12-20220313-1ubuntu1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1 libbinutils_2.38-3ubuntu1 libblas3_3.10.0-2ubuntu1 libblkid1_2.37.2-4ubuntu3 libbrotli1_1.0.9-2build4 libbsd0_0.11.5-1 libbz2-1.0_1.0.8-5 libc-bin_2.35-0ubuntu3 libc-dev-bin_2.35-0ubuntu3 libc6_2.35-0ubuntu3 libc6-dev_2.35-0ubuntu3 libcap-ng0_0.7.9-2.2build3 libcap2_1:2.44-1build2 libcapnp-0.8.0_0.8.0-2ubuntu2 libcc1-0_12-20220313-1ubuntu1 libcom-err2_1.46.5-2ubuntu1 libcrypt-dev_1:4.4.27-1 libcrypt1_1:4.4.27-1 libcryptsetup12_2:2.4.3-1ubuntu1 libctf-nobfd0_2.38-3ubuntu1 libctf0_2.38-3ubuntu1 libcurl3-gnutls_7.81.0-1 libdb5.3_5.3.28+dfsg1-0.8ubuntu2 libdebconfclient0_0.261ubuntu1 libdebhelper-perl_13.6ubuntu1 libdeflate0_1.10-1ubuntu1 libdevmapper1.02.1_2:1.02.175-2.1ubuntu4 libdpkg-perl_1.21.1ubuntu1 libdw1_0.186-1 libedit2_3.1-20210910-1 libelf1_0.186-1 libexpat1_2.4.7-1 libexpat1-dev_2.4.7-1 libext2fs2_1.46.5-2ubuntu1 libfakeroot_1.28-1ubuntu1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libfml-dev_0.1+git20190320.b499514-1 libfml0_0.1+git20190320.b499514-1 libfontconfig1_2.13.1-4.2ubuntu4 libfreetype6_2.11.1+dfsg-1 libfribidi0_1.0.8-2ubuntu2 libgcc-11-dev_11.2.0-18ubuntu1 libgcc-s1_12-20220313-1ubuntu1 libgcrypt20_1.9.4-3ubuntu2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran5_12-20220313-1ubuntu1 libglib2.0-0_2.71.3-1 libgmp10_2:6.2.1+dfsg-3ubuntu1 libgnutls30_3.7.3-4ubuntu1 libgomp1_12-20220313-1ubuntu1 libgpg-error0_1.43-3 libgraphite2-3_1.3.14-1build1 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.19.2-2 libharfbuzz0b_2.7.4-1ubuntu3 libhogweed6_3.7.3-1build1 libhts3_1.13+ds-2build1 libhtscodecs2_1.1.1-3 libicu70_70.1-2 libidn2-0_2.3.2-2 libimagequant0_2.17.0-1 libip4tc2_1.8.7-1ubuntu4 libisl23_0.24-2 libjbig0_2.1-3.1build2 libjpeg-turbo8_2.1.2-0ubuntu1 libjpeg8_8c-2ubuntu8 libjs-jquery_3.6.0+dfsg+~3.5.13-1 libjs-jquery-ui_1.13.1+dfsg-1 libjs-sphinxdoc_4.3.2-1 libjs-underscore_1.13.2~dfsg-2 libjson-c5_0.15-2build3 libk5crypto3_1.19.2-2 libkeyutils1_1.6.1-2ubuntu3 libkmod2_29-1ubuntu1 libkrb5-3_1.19.2-2 libkrb5support0_1.19.2-2 liblapack3_3.10.0-2ubuntu1 liblbfgsb0_3.0+dfsg.3-10 liblcms2-2_2.12~rc1-2build1 libldap-2.5-0_2.5.11+dfsg-1~exp1ubuntu3 liblocale-gettext-perl_1.07-4build3 liblockfile-bin_1.17-1build1 liblockfile1_1.17-1build1 liblz4-1_1.9.3-2build1 liblzma5_5.2.5-2build1 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmd0_1.0.4-1 libminimap-dev_0.2-6 libminimap0_0.2-6 libmount1_2.37.2-4ubuntu3 libmpc3_1.2.1-1 libmpdec3_2.5.1-2build1 libmpfr6_4.1.0-3build2 libmurmurhash2_1.5-3 libncurses6_6.3-2 libncursesw6_6.3-2 libnettle8_3.7.3-1build1 libnghttp2-14_1.43.0-1build2 libnpth0_1.6-3build1 libnsl-dev_1.3.0-2build1 libnsl2_1.3.0-2build1 libopenjp2-7_2.4.0-6 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-11ubuntu1 libpam-modules-bin_1.4.0-11ubuntu1 libpam-runtime_1.4.0-11ubuntu1 libpam0g_1.4.0-11ubuntu1 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13build4 libperl5.32_5.32.1-3ubuntu3 libperl5.34_5.34.0-3ubuntu1 libpipeline1_1.5.5-1 libpng16-16_1.6.37-3build4 libprocps8_2:3.3.17-6ubuntu2 libpsl5_0.21.0-1.2build1 libpython3-all-dev_3.10.1-0ubuntu2 libpython3-dev_3.10.1-0ubuntu2 libpython3-stdlib_3.10.1-0ubuntu2 libpython3.10_3.10.3-1 libpython3.10-dev_3.10.3-1 libpython3.10-minimal_3.10.3-1 libpython3.10-stdlib_3.10.3-1 libqhull-r8.0_2020.2-4 libraqm0_0.7.0-4ubuntu1 libreadline8_8.1.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2build3 libruby3.0_3.0.2-7ubuntu1 libsasl2-2_2.1.27+dfsg2-3ubuntu1 libsasl2-modules-db_2.1.27+dfsg2-3ubuntu1 libseccomp2_2.5.3-2ubuntu1 libselinux1_3.3-1build1 libsemanage-common_3.3-1build2 libsemanage2_3.3-1build2 libsepol1_3.1-1ubuntu2 libsepol2_3.3-1 libsigsegv2_2.13-1ubuntu2 libsmartcols1_2.37.2-4ubuntu3 libsqlite3-0_3.37.2-2 libss2_1.46.5-2ubuntu1 libssh-4_0.9.6-2 libssl1.1_1.1.1l-1ubuntu1 libssl3_3.0.1-0ubuntu1 libstdc++-11-dev_11.2.0-18ubuntu1 libstdc++6_12-20220313-1ubuntu1 libsub-override-perl_0.09-2 libsystemd0_249.11-0ubuntu1 libtasn1-6_4.18.0-4 libtcl8.6_8.6.12+dfsg-1 libtiff5_4.3.0-6 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtk8.6_8.6.12-1 libtool_2.4.6-15build1 libuchardet0_0.0.7-1build1 libudev1_249.11-0ubuntu1 libunistring2_1.0-1 libuuid1_2.37.2-4ubuntu3 libwebp7_1.2.2-2 libwebpdemux2_1.2.2-2 libwebpmux3_1.2.2-2 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libxau6_1:1.0.9-1build4 libxcb1_1.14-3ubuntu2 libxdmcp6_1:1.1.3-0ubuntu4 libxext6_2:1.3.4-1 libxft2_2.3.3-0ubuntu4 libxml2_2.9.13+dfsg-1 libxrender1_1:0.9.10-1build3 libxslt1.1_1.1.34-4build1 libxss1_1:1.2.3-1build1 libxxhash0_0.8.1-1 libyaml-0-2_0.2.2-1build1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.15.0-23.23 lockfile-progs_0.1.19 login_1:4.8.1-2ubuntu2 logsave_1.46.5-2ubuntu1 lsb-base_11.1.0ubuntu3 lto-disabled-list_23 m4_1.4.18-5ubuntu1 mailcap_3.70+nmu1ubuntu1 make_4.3-4.1build1 man-db_2.10.1-1 mash_2.3+dfsg-1build2 mawk_1.3.4.20200120-3 media-types_6.0.0 mime-support_3.66 mount_2.37.2-4ubuntu3 mummer_3.23+dfsg-7 ncurses-base_6.3-2 ncurses-bin_6.3-2 openssl_3.0.1-0ubuntu1 optipng_0.7.7-2 passwd_1:4.8.1-2ubuntu2 patch_2.7.6-7build1 perl_5.34.0-3ubuntu1 perl-base_5.34.0-3ubuntu1 perl-modules-5.32_5.32.1-3ubuntu3 perl-modules-5.34_5.34.0-3ubuntu1 pinentry-curses_1.1.1-1build1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-6ubuntu2 python-matplotlib-data_3.5.1-2build1 python3_3.10.1-0ubuntu2 python3-all_3.10.1-0ubuntu2 python3-all-dev_3.10.1-0ubuntu2 python3-appdirs_1.4.4-2 python3-attr_21.2.0-1 python3-biopython_1.79+dfsg-2 python3-brotli_1.0.9-2build4 python3-bs4_4.10.0-2 python3-cycler_0.11.0-1 python3-dateutil_2.8.1-6 python3-decorator_4.4.2-0ubuntu1 python3-dendropy_4.5.2-1 python3-dev_3.10.1-0ubuntu2 python3-distutils_3.10.3-0ubuntu2 python3-fonttools_4.29.1-2build1 python3-fs_2.4.12-1 python3-importlib-metadata_4.6.4-1 python3-iniconfig_1.1.1-2 python3-kiwisolver_1.3.2-1 python3-lib2to3_3.10.3-0ubuntu2 python3-lxml_4.8.0-1build1 python3-lz4_3.1.3+dfsg-1build2 python3-matplotlib_3.5.1-2build1 python3-minimal_3.10.1-0ubuntu2 python3-more-itertools_8.10.0-2 python3-mpmath_1.2.1-2 python3-numpy_1:1.21.5-1build1 python3-packaging_21.3-1 python3-pil_9.0.1-1 python3-pil.imagetk_9.0.1-1 python3-pkg-resources_59.6.0-1.2 python3-pluggy_0.13.0-7.1 python3-py_1.10.0-1 python3-pymummer_0.11.0-2 python3-pyparsing_2.4.7-1 python3-pysam_0.17.0+ds-2build1 python3-pytest_6.2.5-1ubuntu2 python3-renderpm_3.6.8-1 python3-reportlab_3.6.8-1 python3-reportlab-accel_3.6.8-1 python3-scipy_1.8.0-1exp2build1 python3-setuptools_59.6.0-1.2 python3-six_1.16.0-3 python3-soupsieve_2.3.1-1 python3-sympy_1.9-1 python3-tk_3.10.3-0ubuntu2 python3-toml_0.10.2-1 python3-tz_2021.3-1 python3-ufolib2_0.13.1+dfsg1-1 python3-unicodedata2_14.0.0+ds-8 python3-zipp_1.0.0-3 python3.10_3.10.3-1 python3.10-dev_3.10.3-1 python3.10-minimal_3.10.3-1 rake_13.0.6-2 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-0ubuntu5 ruby_1:3.0~exp1 ruby-asciidoctor_2.0.16-2 ruby-net-telnet_0.1.1-2 ruby-rubygems_3.3.5-2 ruby-xmlrpc_0.3.2-1 ruby3.0_3.0.2-7ubuntu1 rubygems-integration_1.18 samtools_1.13-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1ubuntu1 sensible-utils_0.0.17 sgml-base_1.30 systemd_249.11-0ubuntu1 systemd-sysv_249.11-0ubuntu1 systemd-timesyncd_249.11-0ubuntu1 sysvinit-utils_3.01-1ubuntu1 tar_1.34+dfsg-1build2 tk8.6-blt2.5_2.5.3+dfsg-4.1build1 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 ucf_3.0043 unicode-data_14.0.0-1.1 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu3 w3-dtd-mathml_2.0.0.0-5.1 x11-common_1:7.7+23ubuntu1 xml-core_0.18+nmu1 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu8 zlib1g-dev_1:1.2.11.dfsg-2ubuntu8 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: ariba Binary: ariba Architecture: any Version: 2.14.6+ds-3build1 Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Homepage: https://github.com/sanger-pathogens/ariba Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/ariba Vcs-Git: https://salsa.debian.org/med-team/ariba.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), dh-python, python3-biopython, python3-all-dev, python3-dendropy, python3-setuptools, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3-pytest, 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, spades [amd64] Package-List: ariba deb science optional arch=any Checksums-Sha1: 9e4b9ed6460de8733b121f1a1b9cfa9785c25cb9 1970492 ariba_2.14.6+ds.orig.tar.xz 1515877787595ec27d03b823d6542899374cc1b0 9888 ariba_2.14.6+ds-3build1.debian.tar.xz Checksums-Sha256: b7329ba1983834d3d49a97f838b1fa7e3bdd4556fc45220c75fa7d59c271ec4c 1970492 ariba_2.14.6+ds.orig.tar.xz 5a048091866dbf9b2b83a20df469c3ef6ace6bed68675ce0437b7de9fc138205 9888 ariba_2.14.6+ds-3build1.debian.tar.xz Files: 908a550cb2c7683a271f16aee3f079ad 1970492 ariba_2.14.6+ds.orig.tar.xz 3b3222cc8149e2a707e2274c04a8acd9 9888 ariba_2.14.6+ds-3build1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAmIyOHkACgkQr8/sjmac 4cIZYA//VdIR1CAWzG/PUIHnj/t3IUYc0lu9YZ8H7KgiBcXS3fC5u3k5plisl9nt 6x7T6cj2myjEiHAAuuWYEnG6/JY5dhbwZXdj2a4Q7WR1EjmU2W1Ipa+vjC8Q9cM5 YvOBpsFgsX6yeZEh/X1RPNwWfp7db7ZBap2ZTQy/V+JeQNyWrLQ2ebRbgHCSXx7t k/cFJZ59jAFM7YJAVm4ZAArmqHvMJV+DIYvG2PQIGKGUp3aARn6NORAq05qoyAT9 l3ITIuyoeD5f6rOC8zgCsKljGtpYJTA1OlZHLF3/fPSqKAHShk5MG1GhTCdDF5yI 9zqbPuwlWnX1Ll8SPGBKKNdi+HkUZIZOA0j5DWjltPKWen+oPOneAXpGYCwRjeV4 zDajfJ/qkW/4Cy/Lwu1rlJSwr7ET08rM1Vy2faV5H1FJLHrCUHec9Bk8XN648+he /Z/DDNUxdTG2Zko4a78QfP6s9XMpN25ZfkddP88dw0FT/O3pL21TYp/D/jEnPyXb AxVh0XH3Cprh9YxSy+SbnJfSV3/oJts2o+HT0p2spOSTav7yArdbtr1juEbHDKhG D5tp4O4KGtPmZ9n17TKIzdAuqis9kR8yXT1bHNAniE3rRq5ppBI6POsc3fYYBkJU GLIt+nxabYampIQQ3iZlGUgJ2BFZTV+vOR+QQg96J5SmtlnRExI= =n7/y -----END PGP SIGNATURE----- gpgv: Signature made Wed Mar 16 19:20:25 2022 UTC gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify signature ./ariba_2.14.6+ds-3build1.dsc dpkg-source: info: extracting ariba in /<> dpkg-source: info: unpacking ariba_2.14.6+ds.orig.tar.xz dpkg-source: info: unpacking ariba_2.14.6+ds-3build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_packaged_libs_for_extension.patch dpkg-source: info: applying use_bwa_compatible_fermi-lite.patch dpkg-source: info: applying add-testdata.patch dpkg-source: info: applying disable-tests-with-internet-access.patch dpkg-source: info: applying support-pymummer-0.11.patch dpkg-source: info: applying run-debian-spades-wrapper.patch dpkg-source: info: applying port-to-pytest.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=parallel=8 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-23248863 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-23248863 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-23248863 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -mLaunchpad Build Daemon -B -rfakeroot dpkg-buildpackage: info: source package ariba dpkg-buildpackage: info: source version 2.14.6+ds-3build1 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture riscv64 debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' rm -rf /<>/debian/man dh_auto_clean -- I: pybuild base:237: python3.10 setup.py clean running clean removing '/<>/.pybuild/cpython3_3.10_ariba/build' (and everything under it) 'build/bdist.linux-riscv64' does not exist -- can't clean it 'build/scripts-3.10' does not exist -- can't clean it make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules binary-arch dh binary-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:237: python3.10 setup.py config running config dh_auto_build -a -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3 setup.py build running build running build_py creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/__init__.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/versions.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/report_filter.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/cluster.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/megares_data_finder.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/cdhit.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/mic_plotter.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/samtools_variants.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/sequence_variant.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/tb.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/assembly_compare.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/aln_to_metadata.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/summary_sample.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/mapping.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/read_store.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/summary_cluster.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/flag.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/pubmlst_ref_preparer.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/ref_seq_chooser.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/mlst_profile.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/summary_cluster_variant.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/ref_genes_getter.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/vfdb_parser.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/bam_parse.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/assembly.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/clusters.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/scaffold_graph.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/report_flag_expander.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/read_filter.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/refdata_query.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/sequence_metadata.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/faidx.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/mlst_reporter.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/megares_zip_parser.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/common.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/histogram.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/ref_preparer.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/summary.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/card_record.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/link.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/report.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/assembly_variants.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/reference_data.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/external_progs.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba copying ariba/pubmlst_getter.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/__init__.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/megares_data_finder_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/sequence_metadata_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/ref_genes_getter_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/mlst_profile_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/summary_sample_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/cluster_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/ref_seq_chooser_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/report_flag_expander_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/megares_zip_parser_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/tb_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/external_progs_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/ncbi_getter_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/pubmlst_getter_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/reference_data_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/cdhit_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/scaffold_graph_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/common_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/sequence_variant_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/test_refdata_query.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/versions_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/flag_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/assembly_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/pubmlst_ref_preparer_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/read_store_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/ref_preparer_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/assembly_variants_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/histogram_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/bam_parse_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/mapping_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/clusters_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/assembly_compare_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/summary_cluster_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/samtools_variants_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/aln_to_metadata_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/read_filter_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/card_record_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/faidx_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/vfdb_parser_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/report_filter_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/mic_plotter_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/mlst_reporter_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/summary_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/link_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests copying ariba/tests/summary_cluster_variant_test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/version.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/__init__.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/getref.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/run.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/flag.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/expandflag.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/prepareref_tb.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/aln2meta.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/reportfilter.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/pubmlstspecies.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/test.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/refquery.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/pubmlstget.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/summary.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/micplot.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks copying ariba/tasks/prepareref.py -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_seqs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data copying ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data copying ariba/test_run_data/metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data copying ariba/test_run_data/reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.json -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20190102.json -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.gb -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.json -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181221.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data copying ariba/tb_data/panel.20181115.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data copying ariba/tb_data/NC_000962.3.fa.gz -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_fasta_file.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.expected.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.params.json -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.vcf -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_cat_genes_match_ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/tb_report_to_resistance_dict.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_fake_run.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_fofn -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.2.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_write_all_links_to_file.out -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_long.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_write_distance_matrix.distances -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_summary_file.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_load_file.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_sequence_type.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.out -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.2.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.reads.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.in -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_getter.dbases.xml -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.rename -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_data_info_file -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_var_groups.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.2.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.init.profile.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_compress_and_index_file.in -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.profile.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_run.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/tb_genbank_to_gene_coords.gb -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.3.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.out -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_count_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/dummy.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.1 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.ref.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.removed.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_bad.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.3 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_fix_out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_report.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_load_report_good.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_load_mic_file.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.empty.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.out.csv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_write_report.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_bad.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_sam_to_fastq.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_clean.in -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_genes.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_fails.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_sort_file.in -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refdata_query_prepareref.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_load_input_files.1.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_whole_run.in.1.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.no_link_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/report_filter_test_init_good.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_not_gene.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.expected.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_to_matrix.1.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_rename_file.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.read_store -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/vfdb_parser_test_run.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_init_refdata.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_init_ok.rename.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/test_common_cat_files.in.2 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/graph_test_update_from_sam.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_dummy_db.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_profile_test.profile.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_ok.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/refcheck_test_check_too_short.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/summary_test_init.fofn -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_preparer_test_run.in.2.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/read_filter_test_run.in.ref.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/megares_zip_parser_load_annotations.csv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/link_test_init.reads.make_link.bam -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/report_flag_expander.run.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/assembly_run_fermilite.expected.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data copying ariba/tests/data/reference_data_test_rename_sequences.out -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.info.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref copying ariba/tests/data/refdata_query_prepareref/00.rename_info -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out copying ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref copying ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon copying ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail copying ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa copying ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_write_files copying ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_write_files creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 copying ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2 creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir copying ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon copying ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon creating /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 copying ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1 creating /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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 -> /<>/.pybuild/cpython3_3.10_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-riscv64-3.10 creating build/temp.linux-riscv64-3.10/ariba creating build/temp.linux-riscv64-3.10/ariba/ext riscv64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/minimap -I/usr/include/python3.10 -c ariba/ext/minimap_ariba.cpp -o build/temp.linux-riscv64-3.10/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); | ~~~~~~^~~~~~~~~~~~~~ riscv64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.10/ariba/ext/minimap_ariba.o -o /<>/.pybuild/cpython3_3.10_ariba/build/minimap_ariba.cpython-310-riscv64-linux-gnu.so -lz -lminimap building 'fermilite_ariba' extension riscv64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c ariba/ext/fml-asm_ariba.cpp -o build/temp.linux-riscv64-3.10/ariba/ext/fml-asm_ariba.o riscv64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.10/ariba/ext/fml-asm_ariba.o -o /<>/.pybuild/cpython3_3.10_ariba/build/fermilite_ariba.cpython-310-riscv64-linux-gnu.so -lz -lfml building 'vcfcall_ariba' extension riscv64-linux-gnu-gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.10 -c ariba/ext/vcfcall_ariba.cpp -o build/temp.linux-riscv64-3.10/ariba/ext/vcfcall_ariba.o riscv64-linux-gnu-g++ -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-riscv64-3.10/ariba/ext/vcfcall_ariba.o -o /<>/.pybuild/cpython3_3.10_ariba/build/vcfcall_ariba.cpython-310-riscv64-linux-gnu.so running build_scripts creating build/scripts-3.10 copying and adjusting scripts/ariba -> build/scripts-3.10 changing mode of build/scripts-3.10/ariba from 644 to 755 dh: command-omitted: The call to "dh_auto_test -a -O--buildsystem=pybuild" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_testroot -a -O--buildsystem=pybuild dh_prep -a -O--buildsystem=pybuild dh_auto_install --destdir=debian/ariba/ -a -O--buildsystem=pybuild I: pybuild base:237: /usr/bin/python3 setup.py install --root /<>/debian/ariba running install /usr/lib/python3/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. warnings.warn( running build running build_py running build_ext running build_scripts running install_lib creating /<>/debian/ariba/usr creating /<>/debian/ariba/usr/lib creating /<>/debian/ariba/usr/lib/python3.10 creating /<>/debian/ariba/usr/lib/python3.10/dist-packages copying /<>/.pybuild/cpython3_3.10_ariba/build/fermilite_ariba.cpython-310-riscv64-linux-gnu.so -> /<>/debian/ariba/usr/lib/python3.10/dist-packages copying /<>/.pybuild/cpython3_3.10_ariba/build/vcfcall_ariba.cpython-310-riscv64-linux-gnu.so -> /<>/debian/ariba/usr/lib/python3.10/dist-packages copying /<>/.pybuild/cpython3_3.10_ariba/build/minimap_ariba.cpython-310-riscv64-linux-gnu.so -> /<>/debian/ariba/usr/lib/python3.10/dist-packages creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/__init__.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/versions.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/report_filter.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/cluster.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/megares_data_finder.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/cdhit.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/mic_plotter.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/samtools_variants.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/sequence_variant.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/test_run_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data/ref_seqs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/test_run_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/test_run_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/test_run_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data/metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/test_run_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/test_run_data/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/test_run_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/assembly_compare.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/aln_to_metadata.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/__init__.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/megares_data_finder_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/sequence_metadata_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/ref_genes_getter_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/mlst_profile_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/summary_sample_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/cluster_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/ref_seq_chooser_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/report_flag_expander_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/megares_zip_parser_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/tb_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/external_progs_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_sequence.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_fasta_file.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_sequence_type.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.het_snp.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_init_ok.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/report_filter_test_run.expected.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_init_ok.params.json -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.vcf -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_cat_genes_match_ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/tb_report_to_resistance_dict.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/pubmlst_rename_seqs.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_sequence.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_fake_run.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_test_load_fofn -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_test_whole_run.in.2.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_init_ok.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_run_fermilite_fails.expected.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/graph_test_write_all_links_to_file.out -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_check_too_long.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_total_depth_per_contig -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_test_write_distance_matrix.distances -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_load_summary_file.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_parse.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_sample_test_load_file.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.properPairs -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.good -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_sequence_type.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_parse.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads.make_link_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_init_fails.empty.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/test_common_cat_files.out -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_to_matrix.2.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads.no_link_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_run_fermilite.reads.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_get_reads.in -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/pubmlst_getter.dbases.xml -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_fix_out.rename -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_load_data_info_file -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_sample_test_var_groups.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_fix_in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_delete_codon.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads.no_link.bam.bai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_count_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_make_cluster_file.out -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_test_load_input_files.2.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/megares_zip_parser_write_files copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_profile_test.init.profile.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.in.1.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_compress_and_index_file.in -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/vfdb_parser_test_run.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.profile.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/report_filter_test_run.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/tb_genbank_to_gene_coords.gb -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_fix_out.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_metadata_tsv.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_run.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_check_duplicate_name.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/report_flag_expander.run.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_rename_sequences.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.in.3.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_sort_file.out -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_count_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/dummy.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/test_common_cat_files.in.1 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.ref.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/graph_test_update_from_sam.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/00.info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref/00.rename_info -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/refdata_query_prepareref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_sorted.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_sample_test_column_summary_data.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_fix_out.removed.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/report_filter_test_load_report_bad.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/test_common_cat_files.in.3 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_fix_out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_report.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_dummy_db.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/report_filter_test_load_report_good.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_dummy_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_load_mic_file.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_init_fails.empty.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_test_whole_run.out.csv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/report_filter_test_write_report.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/report_filter_test_init_bad.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_sam_to_fastq.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_remove_bad_genes.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_get_total_alignment_score.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_insert_codon.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_clean.in -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_remove_bad_genes.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_init_fails.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_dummy_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_refdata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_sort_file.in -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads.make_link_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refdata_query_prepareref.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_test_load_input_files.1.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_gene_fa.db.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_test_whole_run.in.1.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads.no_link_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.ref/00.params.json -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/clusters_run_with_tb.ref copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/report_filter_test_init_good.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_check_not_gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_check_spades_log_file.log.bad -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data.expected.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_to_matrix.1.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_rename_file.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.het_snp.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_test_run.in.read_store -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/vfdb_parser_test_run.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_refdata.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_write_files.expect.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_test_run.in.reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/faidx_test_write_fa_subset.out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_init_ok.rename.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/test_common_cat_files.in.2 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/pubmlst_rename_seqs.expected.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/graph_test_update_from_sam.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.het_snps.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_dummy_db.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_profile_test.profile.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam.bai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_check_ok.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_parse.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/refcheck_test_check_too_short.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/summary_test_init.fofn -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.in.4.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2 copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cdhit_test_load_user_clusters_file.good -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_preparer_test_run.in.2.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/read_filter_test_run.in.ref.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/megares_zip_parser_load_annotations.csv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/link_test_init.reads.make_link.bam -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/report_flag_expander.run.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/assembly_run_fermilite.expected.log -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/data/reference_data_test_rename_sequences.out -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/ncbi_getter_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/pubmlst_getter_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/reference_data_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/cdhit_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/scaffold_graph_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/common_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/sequence_variant_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/test_refdata_query.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/versions_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/flag_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/assembly_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/pubmlst_ref_preparer_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/read_store_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/ref_preparer_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/assembly_variants_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/histogram_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/bam_parse_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/mapping_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/clusters_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/assembly_compare_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/summary_cluster_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/samtools_variants_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/aln_to_metadata_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/read_filter_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/card_record_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/faidx_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/vfdb_parser_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/report_filter_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/mic_plotter_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/mlst_reporter_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/summary_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/link_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tests/summary_cluster_variant_test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/summary_sample.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/mapping.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/read_store.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/summary_cluster.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/flag.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/pubmlst_ref_preparer.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/ref_seq_chooser.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/mlst_profile.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/summary_cluster_variant.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/ref_genes_getter.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/vfdb_parser.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/bam_parse.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/assembly.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data/panel.20181115.json -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data/panel.20190102.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data/panel.20190102.json -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data/NC_000962.3.gb -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data/panel.20181221.json -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data/panel.20181221.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data/panel.20181115.txt -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tb_data/NC_000962.3.fa.gz -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb_data copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/clusters.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/scaffold_graph.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/report_flag_expander.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/read_filter.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/refdata_query.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/sequence_metadata.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/faidx.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/mlst_reporter.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba creating /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/version.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/__init__.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/getref.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/run.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/flag.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/expandflag.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/prepareref_tb.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/aln2meta.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/reportfilter.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/pubmlstspecies.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/test.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/refquery.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/pubmlstget.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/summary.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/micplot.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/tasks/prepareref.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/megares_zip_parser.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/common.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/histogram.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/ref_preparer.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/summary.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/card_record.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/link.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/report.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/assembly_variants.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/reference_data.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/external_progs.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba copying /<>/.pybuild/cpython3_3.10_ariba/build/ariba/pubmlst_getter.py -> /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/versions.py to versions.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/report_filter.py to report_filter.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/cluster.py to cluster.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/megares_data_finder.py to megares_data_finder.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/cdhit.py to cdhit.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/mic_plotter.py to mic_plotter.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/samtools_variants.py to samtools_variants.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/sequence_variant.py to sequence_variant.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tb.py to tb.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/assembly_compare.py to assembly_compare.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/aln_to_metadata.py to aln_to_metadata.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/megares_data_finder_test.py to megares_data_finder_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/sequence_metadata_test.py to sequence_metadata_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/ref_genes_getter_test.py to ref_genes_getter_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/mlst_profile_test.py to mlst_profile_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/summary_sample_test.py to summary_sample_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/cluster_test.py to cluster_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/ref_seq_chooser_test.py to ref_seq_chooser_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/report_flag_expander_test.py to report_flag_expander_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/megares_zip_parser_test.py to megares_zip_parser_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/tb_test.py to tb_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/external_progs_test.py to external_progs_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/ncbi_getter_test.py to ncbi_getter_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/pubmlst_getter_test.py to pubmlst_getter_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/reference_data_test.py to reference_data_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/cdhit_test.py to cdhit_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/scaffold_graph_test.py to scaffold_graph_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/common_test.py to common_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/sequence_variant_test.py to sequence_variant_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/test_refdata_query.py to test_refdata_query.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/versions_test.py to versions_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/flag_test.py to flag_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/assembly_test.py to assembly_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py to pubmlst_ref_preparer_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/read_store_test.py to read_store_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/ref_preparer_test.py to ref_preparer_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/assembly_variants_test.py to assembly_variants_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/histogram_test.py to histogram_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/bam_parse_test.py to bam_parse_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/mapping_test.py to mapping_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/clusters_test.py to clusters_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/assembly_compare_test.py to assembly_compare_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/summary_cluster_test.py to summary_cluster_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/samtools_variants_test.py to samtools_variants_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/aln_to_metadata_test.py to aln_to_metadata_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/read_filter_test.py to read_filter_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/card_record_test.py to card_record_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/faidx_test.py to faidx_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/vfdb_parser_test.py to vfdb_parser_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/report_filter_test.py to report_filter_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/mic_plotter_test.py to mic_plotter_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/mlst_reporter_test.py to mlst_reporter_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/summary_test.py to summary_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/link_test.py to link_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tests/summary_cluster_variant_test.py to summary_cluster_variant_test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/summary_sample.py to summary_sample.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/mapping.py to mapping.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/read_store.py to read_store.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/summary_cluster.py to summary_cluster.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/flag.py to flag.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/pubmlst_ref_preparer.py to pubmlst_ref_preparer.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/ref_seq_chooser.py to ref_seq_chooser.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/mlst_profile.py to mlst_profile.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/summary_cluster_variant.py to summary_cluster_variant.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/ref_genes_getter.py to ref_genes_getter.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/vfdb_parser.py to vfdb_parser.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/bam_parse.py to bam_parse.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/assembly.py to assembly.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/clusters.py to clusters.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/scaffold_graph.py to scaffold_graph.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/report_flag_expander.py to report_flag_expander.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/read_filter.py to read_filter.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/refdata_query.py to refdata_query.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/sequence_metadata.py to sequence_metadata.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/faidx.py to faidx.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/mlst_reporter.py to mlst_reporter.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/version.py to version.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/__init__.py to __init__.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/getref.py to getref.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/run.py to run.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/flag.py to flag.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/expandflag.py to expandflag.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/prepareref_tb.py to prepareref_tb.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/aln2meta.py to aln2meta.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/reportfilter.py to reportfilter.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/pubmlstspecies.py to pubmlstspecies.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/test.py to test.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/refquery.py to refquery.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/pubmlstget.py to pubmlstget.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/summary.py to summary.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/micplot.py to micplot.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/tasks/prepareref.py to prepareref.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/megares_zip_parser.py to megares_zip_parser.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/common.py to common.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/histogram.py to histogram.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/ref_preparer.py to ref_preparer.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/summary.py to summary.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/card_record.py to card_record.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/link.py to link.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/report.py to report.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/assembly_variants.py to assembly_variants.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/reference_data.py to reference_data.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/external_progs.py to external_progs.cpython-310.pyc byte-compiling /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba/pubmlst_getter.py to pubmlst_getter.cpython-310.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' adding license file 'LICENSE' adding license file 'AUTHORS' writing manifest file 'ariba.egg-info/SOURCES.txt' Copying ariba.egg-info to /<>/debian/ariba/usr/lib/python3.10/dist-packages/ariba-2.14.6.egg-info Skipping SOURCES.txt running install_scripts creating /<>/debian/ariba/usr/bin copying build/scripts-3.10/ariba -> /<>/debian/ariba/usr/bin changing mode of /<>/debian/ariba/usr/bin/ariba to 755 dh_installdocs -a -O--buildsystem=pybuild dh_installchangelogs -a -O--buildsystem=pybuild debian/rules override_dh_installman make[1]: Entering directory '/<>' mkdir -p /<>/debian/man asciidoctor -a docdate='' -b manpage -o /<>/debian/man/ariba.1 /<>/debian/ariba.1.adoc dh_installman -- make[1]: Leaving directory '/<>' dh_python3 -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 debugedit: debian/ariba/usr/lib/python3/dist-packages/fermilite_ariba.cpython-310-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f20 b4ac6dbcce1c71587a59f27ec643155efe2d5e33 debugedit: debian/ariba/usr/lib/python3/dist-packages/vcfcall_ariba.cpython-310-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 8b6c23fbc4c449079dfe0e8ea41030ea2e26878c debugedit: debian/ariba/usr/lib/python3/dist-packages/minimap_ariba.cpython-310-riscv64-linux-gnu.so: Unknown DWARF DW_FORM_0x1f21 17cdcfb0ebe2aabf349815ca2e2f890b0ba9fa77 dh_makeshlibs -a -O--buildsystem=pybuild dh_shlibdeps -a -O--buildsystem=pybuild 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 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing ariba-dbgsym (in debian/.debhelper/ariba/dbgsym-root); do_strip: , oemstrip: pkgstriptranslations: processing ariba (in debian/ariba); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/.debhelper/ariba/dbgsym-root/DEBIAN/control, package ariba-dbgsym, directory debian/.debhelper/ariba/dbgsym-root dpkg-deb: building package 'ariba-dbgsym' in 'debian/.debhelper/scratch-space/build-ariba/ariba-dbgsym_2.14.6+ds-3build1_riscv64.deb'. pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " Renaming ariba-dbgsym_2.14.6+ds-3build1_riscv64.deb to ariba-dbgsym_2.14.6+ds-3build1_riscv64.ddeb pkgstripfiles: processing control file: debian/ariba/DEBIAN/control, package ariba, directory debian/ariba pkgstripfiles: Truncating usr/share/doc/ariba/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 8 cpus) for package ariba ... pkgstripfiles: No PNG files. dpkg-deb: building package 'ariba' in '../ariba_2.14.6+ds-3build1_riscv64.deb'. dpkg-genbuildinfo --build=any -O../ariba_2.14.6+ds-3build1_riscv64.buildinfo dpkg-genchanges --build=any -mLaunchpad Build Daemon -O../ariba_2.14.6+ds-3build1_riscv64.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 2022-03-17T17:52:51Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ ariba_2.14.6+ds-3build1_riscv64.changes: ---------------------------------------- Format: 1.8 Date: Wed, 16 Mar 2022 19:20:24 +0000 Source: ariba Binary: ariba Built-For-Profiles: noudeb Architecture: riscv64 Version: 2.14.6+ds-3build1 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Graham Inggs Description: ariba - Antibiotic Resistance Identification By Assembly Changes: ariba (2.14.6+ds-3build1) jammy; urgency=medium . * No-change rebuild with Python 3.10 only Checksums-Sha1: 6e0d9db2674317889b179f0d2b0151ff726ee9e7 319468 ariba-dbgsym_2.14.6+ds-3build1_riscv64.ddeb 8cafc0c38f958ff931ec8f4621927fd6ffafb62e 11136 ariba_2.14.6+ds-3build1_riscv64.buildinfo 16b6cbba663dea7acbef5ba2f7cbff6f2cbe5b7f 2044670 ariba_2.14.6+ds-3build1_riscv64.deb Checksums-Sha256: 213a1fa7ee9f9ec7ac41029a95aaa91008401899b8896dd3a9e0f4d45bf91555 319468 ariba-dbgsym_2.14.6+ds-3build1_riscv64.ddeb a41e9e737f85f1c7de6703ef4b31c0d41aec4d505defadedb0b803adae6eb642 11136 ariba_2.14.6+ds-3build1_riscv64.buildinfo d9efb6c8e00c35f52a99e2f9c81bf4781b74fd9207f8674e95c13b8ec1081869 2044670 ariba_2.14.6+ds-3build1_riscv64.deb Files: 69e5392467542c37bc17ecee47e134fa 319468 debug optional ariba-dbgsym_2.14.6+ds-3build1_riscv64.ddeb e86391f08b42b682c5782fb5521ffb56 11136 science optional ariba_2.14.6+ds-3build1_riscv64.buildinfo f1f0586772e22869e58e0ba61e8befb4 2044670 science optional ariba_2.14.6+ds-3build1_riscv64.deb /<>/ariba_2.14.6+ds-3build1_riscv64.changes.new could not be renamed to /<>/ariba_2.14.6+ds-3build1_riscv64.changes: Illegal seek Distribution field may be wrong!!! +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: ariba Binary: ariba ariba-dbgsym Architecture: riscv64 Version: 2.14.6+ds-3build1 Checksums-Md5: 69e5392467542c37bc17ecee47e134fa 319468 ariba-dbgsym_2.14.6+ds-3build1_riscv64.ddeb f1f0586772e22869e58e0ba61e8befb4 2044670 ariba_2.14.6+ds-3build1_riscv64.deb Checksums-Sha1: 6e0d9db2674317889b179f0d2b0151ff726ee9e7 319468 ariba-dbgsym_2.14.6+ds-3build1_riscv64.ddeb 16b6cbba663dea7acbef5ba2f7cbff6f2cbe5b7f 2044670 ariba_2.14.6+ds-3build1_riscv64.deb Checksums-Sha256: 213a1fa7ee9f9ec7ac41029a95aaa91008401899b8896dd3a9e0f4d45bf91555 319468 ariba-dbgsym_2.14.6+ds-3build1_riscv64.ddeb d9efb6c8e00c35f52a99e2f9c81bf4781b74fd9207f8674e95c13b8ec1081869 2044670 ariba_2.14.6+ds-3build1_riscv64.deb Build-Origin: Ubuntu Build-Architecture: riscv64 Build-Date: Thu, 17 Mar 2022 17:52:44 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: asciidoctor (= 2.0.16-2), autoconf (= 2.71-2), automake (= 1:1.16.5-1.1ubuntu4), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20220109.1), base-files (= 12ubuntu2), base-passwd (= 3.5.52), bash (= 5.1-6ubuntu1), binutils (= 2.38-3ubuntu1), binutils-common (= 2.38-3ubuntu1), binutils-riscv64-linux-gnu (= 2.38-3ubuntu1), blt (= 2.5.3+dfsg-4.1build1), bowtie2 (= 2.4.5-1), bsdextrautils (= 2.37.2-4ubuntu3), bsdutils (= 1:2.37.2-4ubuntu3), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-5), ca-certificates (= 20211016), cd-hit (= 4.8.1-4), coreutils (= 8.32-4.1ubuntu1), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-18ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79ubuntu1), debhelper (= 13.6ubuntu1), debianutils (= 5.5-1ubuntu1), debugedit (= 1:5.0-4), dh-autoreconf (= 20), dh-python (= 5.20220215), dh-strip-nondeterminism (= 1.13.0-1), diffutils (= 1:3.8-0ubuntu1), dpkg (= 1.21.1ubuntu1), dpkg-dev (= 1.21.1ubuntu1), dwz (= 0.14-1build1), fastaq (= 3.17.0-4), file (= 1:5.41-2), findutils (= 4.8.0-1ubuntu2), fontconfig-config (= 2.13.1-4.2ubuntu4), fonts-dejavu-core (= 2.37-2build1), fonts-lyx (= 2.3.6-1), fonts-urw-base35 (= 20200910-1), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-18ubuntu1), gawk (= 1:5.1.0-1build2), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-18ubuntu1), gcc-11-base (= 11.2.0-18ubuntu1), gcc-12-base (= 12-20220313-1ubuntu1), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), grep (= 3.7-1), groff-base (= 1.22.4-8), gzip (= 1.10-4ubuntu2), help2man (= 1.49.1), hostname (= 3.23ubuntu1), init-system-helpers (= 1.62), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.3.1-1), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.2.0-18ubuntu1), libatomic1 (= 12-20220313-1ubuntu1), libattr1 (= 1:2.5.1-1), libaudit-common (= 1:3.0.7-1), libaudit1 (= 1:3.0.7-1), libbinutils (= 2.38-3ubuntu1), libblas3 (= 3.10.0-2ubuntu1), libblkid1 (= 2.37.2-4ubuntu3), libbrotli1 (= 1.0.9-2build4), libbsd0 (= 0.11.5-1), libbz2-1.0 (= 1.0.8-5), libc-bin (= 2.35-0ubuntu3), libc-dev-bin (= 2.35-0ubuntu3), libc6 (= 2.35-0ubuntu3), libc6-dev (= 2.35-0ubuntu3), libcap-ng0 (= 0.7.9-2.2build3), libcap2 (= 1:2.44-1build2), libcapnp-0.8.0 (= 0.8.0-2ubuntu2), libcc1-0 (= 12-20220313-1ubuntu1), libcom-err2 (= 1.46.5-2ubuntu1), libcrypt-dev (= 1:4.4.27-1), libcrypt1 (= 1:4.4.27-1), libctf-nobfd0 (= 2.38-3ubuntu1), libctf0 (= 2.38-3ubuntu1), libcurl3-gnutls (= 7.81.0-1), libdb5.3 (= 5.3.28+dfsg1-0.8ubuntu2), libdebconfclient0 (= 0.261ubuntu1), libdebhelper-perl (= 13.6ubuntu1), libdeflate0 (= 1.10-1ubuntu1), libdpkg-perl (= 1.21.1ubuntu1), libdw1 (= 0.186-1), libedit2 (= 3.1-20210910-1), libelf1 (= 0.186-1), libexpat1 (= 2.4.7-1), libexpat1-dev (= 2.4.7-1), libffi8 (= 3.4.2-4), libfile-stripnondeterminism-perl (= 1.13.0-1), libfml-dev (= 0.1+git20190320.b499514-1), libfml0 (= 0.1+git20190320.b499514-1), libfontconfig1 (= 2.13.1-4.2ubuntu4), libfreetype6 (= 2.11.1+dfsg-1), libfribidi0 (= 1.0.8-2ubuntu2), libgcc-11-dev (= 11.2.0-18ubuntu1), libgcc-s1 (= 12-20220313-1ubuntu1), libgcrypt20 (= 1.9.4-3ubuntu2), libgdbm-compat4 (= 1.23-1), libgdbm6 (= 1.23-1), libgfortran5 (= 12-20220313-1ubuntu1), libglib2.0-0 (= 2.71.3-1), libgmp10 (= 2:6.2.1+dfsg-3ubuntu1), libgnutls30 (= 3.7.3-4ubuntu1), libgomp1 (= 12-20220313-1ubuntu1), libgpg-error0 (= 1.43-3), libgraphite2-3 (= 1.3.14-1build1), libgsl27 (= 2.7.1+dfsg-3), libgslcblas0 (= 2.7.1+dfsg-3), libgssapi-krb5-2 (= 1.19.2-2), libharfbuzz0b (= 2.7.4-1ubuntu3), libhogweed6 (= 3.7.3-1build1), libhts3 (= 1.13+ds-2build1), libhtscodecs2 (= 1.1.1-3), libicu70 (= 70.1-2), libidn2-0 (= 2.3.2-2), libimagequant0 (= 2.17.0-1), libisl23 (= 0.24-2), libjbig0 (= 2.1-3.1build2), libjpeg-turbo8 (= 2.1.2-0ubuntu1), libjpeg8 (= 8c-2ubuntu8), libjs-jquery (= 3.6.0+dfsg+~3.5.13-1), libjs-jquery-ui (= 1.13.1+dfsg-1), libjs-sphinxdoc (= 4.3.2-1), libjs-underscore (= 1.13.2~dfsg-2), libk5crypto3 (= 1.19.2-2), libkeyutils1 (= 1.6.1-2ubuntu3), libkrb5-3 (= 1.19.2-2), libkrb5support0 (= 1.19.2-2), liblapack3 (= 3.10.0-2ubuntu1), liblbfgsb0 (= 3.0+dfsg.3-10), liblcms2-2 (= 2.12~rc1-2build1), libldap-2.5-0 (= 2.5.11+dfsg-1~exp1ubuntu3), liblocale-gettext-perl (= 1.07-4build3), liblz4-1 (= 1.9.3-2build1), liblzma5 (= 5.2.5-2build1), libmagic-mgc (= 1:5.41-2), libmagic1 (= 1:5.41-2), libmd0 (= 1.0.4-1), libminimap-dev (= 0.2-6), libminimap0 (= 0.2-6), libmount1 (= 2.37.2-4ubuntu3), libmpc3 (= 1.2.1-1), libmpdec3 (= 2.5.1-2build1), libmpfr6 (= 4.1.0-3build2), libmurmurhash2 (= 1.5-3), libncurses6 (= 6.3-2), libncursesw6 (= 6.3-2), libnettle8 (= 3.7.3-1build1), libnghttp2-14 (= 1.43.0-1build2), libnsl-dev (= 1.3.0-2build1), libnsl2 (= 1.3.0-2build1), libopenjp2-7 (= 2.4.0-6), libp11-kit0 (= 0.24.0-6), libpam-modules (= 1.4.0-11ubuntu1), libpam-modules-bin (= 1.4.0-11ubuntu1), libpam-runtime (= 1.4.0-11ubuntu1), libpam0g (= 1.4.0-11ubuntu1), libpcre2-8-0 (= 10.39-3), libpcre3 (= 2:8.39-13build4), libperl5.34 (= 5.34.0-3ubuntu1), libpipeline1 (= 1.5.5-1), libpng16-16 (= 1.6.37-3build4), libpsl5 (= 0.21.0-1.2build1), libpython3-all-dev (= 3.10.1-0ubuntu2), libpython3-dev (= 3.10.1-0ubuntu2), libpython3-stdlib (= 3.10.1-0ubuntu2), libpython3.10 (= 3.10.3-1), libpython3.10-dev (= 3.10.3-1), libpython3.10-minimal (= 3.10.3-1), libpython3.10-stdlib (= 3.10.3-1), libqhull-r8.0 (= 2020.2-4), libraqm0 (= 0.7.0-4ubuntu1), libreadline8 (= 8.1.2-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build3), libruby3.0 (= 3.0.2-7ubuntu1), libsasl2-2 (= 2.1.27+dfsg2-3ubuntu1), libsasl2-modules-db (= 2.1.27+dfsg2-3ubuntu1), libselinux1 (= 3.3-1build1), libsigsegv2 (= 2.13-1ubuntu2), libsmartcols1 (= 2.37.2-4ubuntu3), libsqlite3-0 (= 3.37.2-2), libssh-4 (= 0.9.6-2), libssl3 (= 3.0.1-0ubuntu1), libstdc++-11-dev (= 11.2.0-18ubuntu1), libstdc++6 (= 12-20220313-1ubuntu1), libsub-override-perl (= 0.09-2), libsystemd0 (= 249.11-0ubuntu1), libtasn1-6 (= 4.18.0-4), libtcl8.6 (= 8.6.12+dfsg-1), libtiff5 (= 4.3.0-6), libtinfo6 (= 6.3-2), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtk8.6 (= 8.6.12-1), libtool (= 2.4.6-15build1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 249.11-0ubuntu1), libunistring2 (= 1.0-1), libuuid1 (= 2.37.2-4ubuntu3), libwebp7 (= 1.2.2-2), libwebpdemux2 (= 1.2.2-2), libwebpmux3 (= 1.2.2-2), libx11-6 (= 2:1.7.2-2), libx11-data (= 2:1.7.2-2), libxau6 (= 1:1.0.9-1build4), libxcb1 (= 1.14-3ubuntu2), libxdmcp6 (= 1:1.1.3-0ubuntu4), libxext6 (= 2:1.3.4-1), libxft2 (= 2.3.3-0ubuntu4), libxml2 (= 2.9.13+dfsg-1), libxrender1 (= 1:0.9.10-1build3), libxslt1.1 (= 1.1.34-4build1), libxss1 (= 1:1.2.3-1build1), libyaml-0-2 (= 0.2.2-1build1), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.15.0-23.23), login (= 1:4.8.1-2ubuntu2), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 23), m4 (= 1.4.18-5ubuntu1), mailcap (= 3.70+nmu1ubuntu1), make (= 4.3-4.1build1), man-db (= 2.10.1-1), mash (= 2.3+dfsg-1build2), mawk (= 1.3.4.20200120-3), media-types (= 6.0.0), mime-support (= 3.66), mummer (= 3.23+dfsg-7), ncurses-base (= 6.3-2), ncurses-bin (= 6.3-2), openssl (= 3.0.1-0ubuntu1), patch (= 2.7.6-7build1), perl (= 5.34.0-3ubuntu1), perl-base (= 5.34.0-3ubuntu1), perl-modules-5.34 (= 5.34.0-3ubuntu1), po-debconf (= 1.0.21+nmu1), python-matplotlib-data (= 3.5.1-2build1), python3 (= 3.10.1-0ubuntu2), python3-all (= 3.10.1-0ubuntu2), python3-all-dev (= 3.10.1-0ubuntu2), python3-appdirs (= 1.4.4-2), python3-attr (= 21.2.0-1), python3-biopython (= 1.79+dfsg-2), python3-brotli (= 1.0.9-2build4), python3-bs4 (= 4.10.0-2), python3-cycler (= 0.11.0-1), python3-dateutil (= 2.8.1-6), python3-decorator (= 4.4.2-0ubuntu1), python3-dendropy (= 4.5.2-1), python3-dev (= 3.10.1-0ubuntu2), python3-distutils (= 3.10.3-0ubuntu2), python3-fonttools (= 4.29.1-2build1), python3-fs (= 2.4.12-1), python3-importlib-metadata (= 4.6.4-1), python3-iniconfig (= 1.1.1-2), python3-kiwisolver (= 1.3.2-1), python3-lib2to3 (= 3.10.3-0ubuntu2), python3-lxml (= 4.8.0-1build1), python3-lz4 (= 3.1.3+dfsg-1build2), python3-matplotlib (= 3.5.1-2build1), python3-minimal (= 3.10.1-0ubuntu2), python3-more-itertools (= 8.10.0-2), python3-mpmath (= 1.2.1-2), python3-numpy (= 1:1.21.5-1build1), python3-packaging (= 21.3-1), python3-pil (= 9.0.1-1), python3-pil.imagetk (= 9.0.1-1), python3-pkg-resources (= 59.6.0-1.2), python3-pluggy (= 0.13.0-7.1), python3-py (= 1.10.0-1), python3-pymummer (= 0.11.0-2), python3-pyparsing (= 2.4.7-1), python3-pysam (= 0.17.0+ds-2build1), python3-pytest (= 6.2.5-1ubuntu2), python3-renderpm (= 3.6.8-1), python3-reportlab (= 3.6.8-1), python3-reportlab-accel (= 3.6.8-1), python3-scipy (= 1.8.0-1exp2build1), python3-setuptools (= 59.6.0-1.2), python3-six (= 1.16.0-3), python3-soupsieve (= 2.3.1-1), python3-sympy (= 1.9-1), python3-tk (= 3.10.3-0ubuntu2), python3-toml (= 0.10.2-1), python3-tz (= 2021.3-1), python3-ufolib2 (= 0.13.1+dfsg1-1), python3-unicodedata2 (= 14.0.0+ds-8), python3-zipp (= 1.0.0-3), python3.10 (= 3.10.3-1), python3.10-dev (= 3.10.3-1), python3.10-minimal (= 3.10.3-1), rake (= 13.0.6-2), readline-common (= 8.1.2-1), rpcsvc-proto (= 1.4.2-0ubuntu5), ruby (= 1:3.0~exp1), ruby-asciidoctor (= 2.0.16-2), ruby-net-telnet (= 0.1.1-2), ruby-rubygems (= 3.3.5-2), ruby-xmlrpc (= 0.3.2-1), ruby3.0 (= 3.0.2-7ubuntu1), rubygems-integration (= 1.18), samtools (= 1.13-4), sed (= 4.8-1ubuntu1), sensible-utils (= 0.0.17), sgml-base (= 1.30), sysvinit-utils (= 3.01-1ubuntu1), tar (= 1.34+dfsg-1build2), tk8.6-blt2.5 (= 2.5.3+dfsg-4.1build1), tzdata (= 2021e-1ubuntu1), ucf (= 3.0043), unicode-data (= 14.0.0-1.1), util-linux (= 2.37.2-4ubuntu3), w3-dtd-mathml (= 2.0.0.0-5.1), x11-common (= 1:7.7+23ubuntu1), xml-core (= 0.18+nmu1), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu8), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu8) Environment: DEB_BUILD_OPTIONS="nocheck parallel=8" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1647458424" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ ariba_2.14.6+ds-3build1_riscv64.deb ----------------------------------- new Debian package, version 2.0. size 2044670 bytes: control archive=17770 bytes. 1153 bytes, 18 lines control 91140 bytes, 756 lines md5sums 251 bytes, 12 lines * postinst #!/bin/sh 400 bytes, 12 lines * prerm #!/bin/sh Package: ariba Version: 2.14.6+ds-3build1 Architecture: riscv64 Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 20419 Depends: fastaq (>= 3.12.0), python3 (<< 3.11), python3 (>= 3.10~), python3-biopython, python3-bs4, python3-dendropy, python3-matplotlib, python3-pymummer (>= 0.10.2), python3-pysam (>= 0.9.1), python3:any, libc6 (>= 2.27), libfml0 (>= 0.1-4~), libgcc-s1 (>= 3.0), libminimap0 (>= 0.2), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), bowtie2 (>= 2.1.0), cd-hit, mash, mummer, python3-tk Suggests: spades 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 2022-03-16 19:20 ./ drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/ drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/bin/ -rwxr-xr-x root/root 26193 2022-03-16 19:20 ./usr/bin/ariba drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/ drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/ drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba-2.14.6.egg-info/ -rw-r--r-- root/root 552 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba-2.14.6.egg-info/PKG-INFO -rw-r--r-- root/root 1 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba-2.14.6.egg-info/dependency_links.txt -rw-r--r-- root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba-2.14.6.egg-info/requires.txt -rw-r--r-- root/root 50 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba-2.14.6.egg-info/top_level.txt drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/ -rw-r--r-- root/root 1063 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/__init__.py -rw-r--r-- root/root 10940 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/aln_to_metadata.py -rw-r--r-- root/root 15088 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/assembly.py -rw-r--r-- root/root 16416 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/assembly_compare.py -rw-r--r-- root/root 15177 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/assembly_variants.py -rw-r--r-- root/root 3586 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/bam_parse.py -rw-r--r-- root/root 3328 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/card_record.py -rw-r--r-- root/root 6274 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/cdhit.py -rw-r--r-- root/root 19456 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/cluster.py -rw-r--r-- root/root 28393 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/clusters.py -rw-r--r-- root/root 2380 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/common.py -rw-r--r-- root/root 5279 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/external_progs.py -rw-r--r-- root/root 324 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/faidx.py -rw-r--r-- root/root 1430 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/flag.py -rw-r--r-- root/root 1339 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/histogram.py -rw-r--r-- root/root 3981 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/link.py -rw-r--r-- root/root 5037 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/mapping.py -rw-r--r-- root/root 2078 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/megares_data_finder.py -rw-r--r-- root/root 6045 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/megares_zip_parser.py -rw-r--r-- root/root 25422 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/mic_plotter.py -rw-r--r-- root/root 2216 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/mlst_profile.py -rw-r--r-- root/root 3975 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/mlst_reporter.py -rw-r--r-- root/root 4060 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/pubmlst_getter.py -rw-r--r-- root/root 3850 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/pubmlst_ref_preparer.py -rw-r--r-- root/root 2508 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/read_filter.py -rw-r--r-- root/root 2968 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/read_store.py -rw-r--r-- root/root 30576 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/ref_genes_getter.py -rw-r--r-- root/root 8690 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/ref_preparer.py -rw-r--r-- root/root 8370 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/ref_seq_chooser.py -rw-r--r-- root/root 3165 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/refdata_query.py -rw-r--r-- root/root 19480 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/reference_data.py -rw-r--r-- root/root 18629 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/report.py -rw-r--r-- root/root 6965 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/report_filter.py -rw-r--r-- root/root 922 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/report_flag_expander.py -rw-r--r-- root/root 5974 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/samtools_variants.py -rw-r--r-- root/root 3466 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/scaffold_graph.py -rw-r--r-- root/root 1992 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/sequence_metadata.py -rw-r--r-- root/root 2544 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/sequence_variant.py -rw-r--r-- root/root 17649 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/summary.py -rw-r--r-- root/root 13284 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/summary_cluster.py -rw-r--r-- root/root 6067 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/summary_cluster_variant.py -rw-r--r-- root/root 2654 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/summary_sample.py drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tasks/ -rw-r--r-- root/root 284 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/__init__.py -rw-r--r-- root/root 327 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/aln2meta.py -rw-r--r-- root/root 173 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/expandflag.py -rw-r--r-- root/root 151 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/flag.py -rw-r--r-- root/root 239 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/getref.py -rw-r--r-- root/root 1239 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/micplot.py -rw-r--r-- root/root 1302 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/prepareref.py -rw-r--r-- root/root 111 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/prepareref_tb.py -rw-r--r-- root/root 238 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/pubmlstget.py -rw-r--r-- root/root 151 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/pubmlstspecies.py -rw-r--r-- root/root 200 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/refquery.py -rw-r--r-- root/root 825 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/reportfilter.py -rw-r--r-- root/root 2311 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/run.py -rw-r--r-- root/root 2356 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/summary.py -rw-r--r-- root/root 2319 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/test.py -rw-r--r-- root/root 170 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tasks/version.py -rw-r--r-- root/root 9927 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tb.py drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tb_data/ -rw-r--r-- root/root 1284530 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tb_data/NC_000962.3.fa.gz -rw-r--r-- root/root 2917328 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tb_data/NC_000962.3.gb -rw-r--r-- root/root 3179910 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tb_data/panel.20181115.json -rw-r--r-- root/root 1100210 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tb_data/panel.20181115.txt -rw-r--r-- root/root 3179863 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tb_data/panel.20181221.json -rw-r--r-- root/root 1100195 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tb_data/panel.20181221.txt -rw-r--r-- root/root 3179888 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tb_data/panel.20190102.json -rw-r--r-- root/root 1100195 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tb_data/panel.20190102.txt drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/test_run_data/ -rw-r--r-- root/root 1248 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/test_run_data/metadata.tsv -rw-r--r-- root/root 110844 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/test_run_data/reads_1.fq -rw-r--r-- root/root 110844 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/test_run_data/reads_2.fq -rw-r--r-- root/root 3573 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/test_run_data/ref_fasta_to_make_reads_from.fa -rw-r--r-- root/root 1394 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/test_run_data/ref_seqs.fa drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/ -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/__init__.py -rw-r--r-- root/root 17407 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/aln_to_metadata_test.py -rw-r--r-- root/root 20285 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/assembly_compare_test.py -rw-r--r-- root/root 7912 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/assembly_test.py -rw-r--r-- root/root 20039 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/assembly_variants_test.py -rw-r--r-- root/root 5091 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/bam_parse_test.py -rw-r--r-- root/root 8598 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/card_record_test.py -rw-r--r-- root/root 7820 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/cdhit_test.py -rw-r--r-- root/root 34821 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/cluster_test.py -rw-r--r-- root/root 15487 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/clusters_test.py -rw-r--r-- root/root 1095 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/common_test.py drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/ -rw-r--r-- root/root 26 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_aln_file.in.fa -rw-r--r-- root/root 42 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_bad.1.tsv -rw-r--r-- root/root 64 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_bad.2.tsv -rw-r--r-- root/root 85 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_load_vars_file_good.tsv -rw-r--r-- root/root 15 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_make_cluster_file.out -rw-r--r-- root/root 110 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.in.fa -rw-r--r-- root/root 54 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.in.tsv -rw-r--r-- root/root 25 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.cluster -rw-r--r-- root/root 101 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.fa -rw-r--r-- root/root 217 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_coding.out.tsv -rw-r--r-- root/root 110 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.in.fa -rw-r--r-- root/root 54 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.in.tsv -rw-r--r-- root/root 25 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.cluster -rw-r--r-- root/root 101 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.fa -rw-r--r-- root/root 217 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/aln_to_metadata_run_noncoding.out.tsv -rw-r--r-- root/root 2805 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.expected.fa -rw-r--r-- root/root 180 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.expected.log -rw-r--r-- root/root 10083 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.reads_1.fq -rw-r--r-- root/root 10083 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite.reads_2.fq -rw-r--r-- root/root 156 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.expected.log -rw-r--r-- root/root 103 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_1.fq -rw-r--r-- root/root 79 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_assemble_with_fermilite_fails.reads_2.fq -rw-r--r-- root/root 268 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_compare_parse_nucmer_coords_file.coords -rw-r--r-- root/root 2823 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.expected.fa -rw-r--r-- root/root 169 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.expected.log -rw-r--r-- root/root 20166 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite.reads.fq -rw-r--r-- root/root 51 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite_fail.reads.fq -rw-r--r-- root/root 145 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_run_fermilite_fails.expected.log -rw-r--r-- root/root 147 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_1.fq -rw-r--r-- root/root 148 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_fails_reads_2.fq -rw-r--r-- root/root 10083 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq -rw-r--r-- root/root 10083 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq -rw-r--r-- root/root 163 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_check_spades_log_file.log.bad -rw-r--r-- root/root 167 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_check_spades_log_file.log.good -rw-r--r-- root/root 1739 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_fix_contig_orientation.in.fa -rw-r--r-- root/root 1739 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_fix_contig_orientation.out.fa -rw-r--r-- root/root 515 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_fix_contig_orientation.ref.fa -rw-r--r-- root/root 1030 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_parse_assembly_bam.assembly.fa -rw-r--r-- root/root 472 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_parse_assembly_bam.bam -rw-r--r-- root/root 1026 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_scaffold_with_sspace_contigs.fa -rw-r--r-- root/root 35266 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_1.fq -rw-r--r-- root/root 35266 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_test_scaffold_with_sspace_reads_2.fq -rw-r--r-- root/root 61 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.fa -rw-r--r-- root/root 255 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_one_var_one_ctg_cdg.tsv -rw-r--r-- root/root 41 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.fa -rw-r--r-- root/root 135 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_one_var_one_ctg_noncdg.tsv -rw-r--r-- root/root 87 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_mummer_variants.none.snps -rw-r--r-- root/root 249 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_mummer_variants.snp.snps -rw-r--r-- root/root 61 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.fa -rw-r--r-- root/root 145 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_variants_presence_absence.snps -rw-r--r-- root/root 58 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_variants_variants_only.fa -rw-r--r-- root/root 136 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/assembly_variants_test_get_variants_variants_only.snps -rw-r--r-- root/root 472 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_parse.bam -rw-r--r-- root/root 399 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_parse.reads_1.fq -rw-r--r-- root/root 399 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_parse.reads_2.fq -rw-r--r-- root/root 1030 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_parse.ref.fa -rw-r--r-- root/root 465 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.bam -rw-r--r-- root/root 734 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.reads.fq -rw-r--r-- root/root 209 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_sam_to_soft_clipped.ref.fa -rw-r--r-- root/root 368 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.bam -rw-r--r-- root/root 393 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.reads.fq -rw-r--r-- root/root 1009 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_soft_clipped_from_sam.ref.fa -rw-r--r-- root/root 565 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.bam -rw-r--r-- root/root 574 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_1.fq -rw-r--r-- root/root 574 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.reads_2.fq -rw-r--r-- root/root 514 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/bam_parse_test_update_unmapped_mates_from_sam.ref.fa -rw-r--r-- root/root 5357 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_best_seq_reads_1.fq -rw-r--r-- root/root 5357 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_best_seq_reads_2.fq -rw-r--r-- root/root 903 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_best_seq_ref.fa -rw-r--r-- root/root 46 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_best_seq_ref.fa.fai -rw-r--r-- root/root 5357 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_1.fq -rw-r--r-- root/root 5357 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_reads_2.fq -rw-r--r-- root/root 903 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa -rw-r--r-- root/root 46 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_get_best_seq_by_alignment_score_ref.fa.fai -rw-r--r-- root/root 5357 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_1.fq -rw-r--r-- root/root 5357 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_total_alignment_score_reads_2.fq -rw-r--r-- root/root 903 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa -rw-r--r-- root/root 46 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/best_seq_chooser_total_alignment_score_ref_seqs.fa.fai -rw-r--r-- root/root 2058 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_fake_run.in.fa -rw-r--r-- root/root 2058 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_fake_run.non-unique.in.fa -rw-r--r-- root/root 120 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_get_clusters_from_bak_file.in -rw-r--r-- root/root 10 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_load_user_clusters_file.bad1 -rw-r--r-- root/root 20 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_load_user_clusters_file.bad2 -rw-r--r-- root/root 20 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_load_user_clusters_file.bad3 -rw-r--r-- root/root 30 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_load_user_clusters_file.good -rw-r--r-- root/root 2058 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_run.in.fa -rw-r--r-- root/root 15 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.clusters -rw-r--r-- root/root 33 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_run_get_clusters_from_dict.in.fa -rw-r--r-- root/root 41 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cdhit_test_run_get_clusters_from_dict_rename.in.fa -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.fa -rw-r--r-- root/root 713 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.ref_for_reads.fa -rw-r--r-- root/root 42 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/reads_2.fq -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_gene/references.fa -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.fa -rw-r--r-- root/root 43 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/reads_2.fq -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_known_smtls_snp_presabs_nonc/references.fa -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.fa -rw-r--r-- root/root 86 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/reads_2.fq -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_known_snp_presabs_nonc/references.fa -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.fa -rw-r--r-- root/root 713 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.ref_for_reads.fa -rw-r--r-- root/root 49 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/reads_2.fq -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_gene/references.fa -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.fa -rw-r--r-- root/root 47 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/reads_2.fq -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.fa -rw-r--r-- root/root 42 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/reads_2.fq -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene/references.fa -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.fa -rw-r--r-- root/root 49 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/reads_2.fq -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2/references.fa -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.fa -rw-r--r-- root/root 42 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/reads_2.fq -rw-r--r-- root/root 108 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_no_snp/references.fa -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.fa -rw-r--r-- root/root 47 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/reads_2.fq -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc/references.fa -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.fa -rw-r--r-- root/root 43 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/reads_2.fq -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_smtls_snp_varonly_nonc_no_snp/references.fa -rw-r--r-- root/root 205 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_full_run_varonly.not_present.always_report.tsv -rw-r--r-- root/root 36 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_count_reads_1.fq -rw-r--r-- root/root 36 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_count_reads_2.fq -rw-r--r-- root/root 426 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail.in.fa -rw-r--r-- root/root 28 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail.in.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail/ -rw-r--r-- root/root 358 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_1.fq -rw-r--r-- root/root 358 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail/reads_2.fq -rw-r--r-- root/root 426 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_assembly_fail/references.fa -rw-r--r-- root/root 92 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.fa -rw-r--r-- root/root 66 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail.in.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail/ -rw-r--r-- root/root 6944 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq -rw-r--r-- root/root 6944 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_2.fq -rw-r--r-- root/root 92 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa -rw-r--r-- root/root 138 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon.fa -rw-r--r-- root/root 67 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon/ -rw-r--r-- root/root 1146 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa -rw-r--r-- root/root 27364 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq -rw-r--r-- root/root 27364 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq -rw-r--r-- root/root 138 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa -rw-r--r-- root/root 129 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon.fa -rw-r--r-- root/root 67 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon/ -rw-r--r-- root/root 1155 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa -rw-r--r-- root/root 27568 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq -rw-r--r-- root/root 27568 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq -rw-r--r-- root/root 129 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa -rw-r--r-- root/root 194 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars.fa -rw-r--r-- root/root 134 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars/ -rw-r--r-- root/root 1134 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa -rw-r--r-- root/root 27186 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq -rw-r--r-- root/root 27186 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq -rw-r--r-- root/root 194 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa -rw-r--r-- root/root 426 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.fa -rw-r--r-- root/root 28 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering.in.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/ -rw-r--r-- root/root 125 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_1.fq -rw-r--r-- root/root 125 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/reads_2.fq -rw-r--r-- root/root 426 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_no_reads_after_filtering/references.fa -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.fa -rw-r--r-- root/root 41 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.metadata.tsv -rw-r--r-- root/root 348 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch.ref_for_reads.fa drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/ -rw-r--r-- root/root 11346 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_1.fq -rw-r--r-- root/root 11346 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/reads_2.fq -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_gene_start_mismatch/references.fa -rw-r--r-- root/root 268 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding.fa -rw-r--r-- root/root 352 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding.metadata.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding/ -rw-r--r-- root/root 4598 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_1.fq -rw-r--r-- root/root 4598 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding/reads_2.fq -rw-r--r-- root/root 268 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_non_coding/references.fa -rw-r--r-- root/root 194 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence.fa -rw-r--r-- root/root 331 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence.metadata.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence/ -rw-r--r-- root/root 4300 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_1.fq -rw-r--r-- root/root 4300 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence/reads_2.fq -rw-r--r-- root/root 194 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_presence_absence/references.fa -rw-r--r-- root/root 188 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only.fa -rw-r--r-- root/root 197 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only.not_present.metadata.tsv -rw-r--r-- root/root 241 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only.present.metadata.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only/ -rw-r--r-- root/root 4345 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_1.fq -rw-r--r-- root/root 4345 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only/reads_2.fq -rw-r--r-- root/root 188 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ok_variants_only/references.fa -rw-r--r-- root/root 117 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly.fa -rw-r--r-- root/root 67 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly/ -rw-r--r-- root/root 23321 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_1.fq -rw-r--r-- root/root 23321 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq -rw-r--r-- root/root 117 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_partial_asmbly/references.fa -rw-r--r-- root/root 410 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.all_refs.fa -rw-r--r-- root/root 268 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa -rw-r--r-- root/root 352 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/ -rw-r--r-- root/root 4598 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq -rw-r--r-- root/root 4598 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq -rw-r--r-- root/root 268 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.fa -rw-r--r-- root/root 43 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/ -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_1.fq -rw-r--r-- root/root 15588 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/reads_2.fq -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_full_run_smtls_snp_varonly_nonc/references.fa drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1/ -rw-r--r-- root/root 27 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1/genes.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_no_reads_1/reads_2.fq drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2/ -rw-r--r-- root/root 27 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2/genes.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_no_reads_2/reads_1.fq drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa/ -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa/reads_1.fq -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_no_refs_fa/reads_2.fq -rw-r--r-- root/root 15 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_refdata.fa -rw-r--r-- root/root 15 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_init_refdata.tsv -rw-r--r-- root/root 211 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_make_reads_for_assembly.in1.fq -rw-r--r-- root/root 231 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_make_reads_for_assembly.in2.fq -rw-r--r-- root/root 148 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_make_reads_for_assembly.out1.fq -rw-r--r-- root/root 162 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/cluster_test_make_reads_for_assembly.out2.fq -rw-r--r-- root/root 42 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_cat_genes_match_ref.fa drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir/ -rw-r--r-- root/root 174 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir/00.info.txt -rw-r--r-- root/root 11 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir/00.params.json -rw-r--r-- root/root 118 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir/01.filter.check_metadata.tsv -rw-r--r-- root/root 97 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.all.fa -rw-r--r-- root/root 135 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_load_ref_data_from_dir/02.cdhit.clusters.pickle -rw-r--r-- root/root 62 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_minimap_reads_to_all_refs.clstrs.tsv -rw-r--r-- root/root 28 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr2rep -rw-r--r-- root/root 42 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.clstr_count -rw-r--r-- root/root 186 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.hist -rw-r--r-- root/root 5 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_minimap_reads_to_all_refs.out.pairs -rw-r--r-- root/root 261842 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_1.fq -rw-r--r-- root/root 261842 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_minimap_reads_to_all_refs.reads_2.fq -rw-r--r-- root/root 32965 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_minimap_reads_to_all_refs.ref.fa -rw-r--r-- root/root 2076 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.reads_1.fq.gz -rw-r--r-- root/root 2073 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.reads_2.fq.gz drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/ -rw-r--r-- root/root 70 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/00.info.txt -rw-r--r-- root/root 13 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/00.params.json -rw-r--r-- root/root 1337 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/00.version_info.txt -rw-r--r-- root/root 87 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_genes.log -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.log -rw-r--r-- root/root 84 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/01.filter.check_metadata.tsv -rw-r--r-- root/root 1269 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.all.fa -rw-r--r-- root/root 97 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.pickle -rw-r--r-- root/root 27 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.clusters.tsv -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.fa -rw-r--r-- root/root 1269 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.gene.varonly.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_run_with_tb.ref/02.cdhit.noncoding.varonly.fa -rw-r--r-- root/root 60 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.fai -rw-r--r-- root/root 1311 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.sma -rw-r--r-- root/root 39756 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_bam_to_clusters_reads.db.fa.smi -rw-r--r-- root/root 63 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_dummy_db.fa -rw-r--r-- root/root 12 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_dummy_db.tsv -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_dummy_reads_1.fq -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_dummy_reads_2.fq -rw-r--r-- root/root 174 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_load_data_info_file -rw-r--r-- root/root 15 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_load_minimap_files.cluster2representative -rw-r--r-- root/root 20 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_load_minimap_files.clusterCounts -rw-r--r-- root/root 38 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_load_minimap_files.insertHistogram -rw-r--r-- root/root 9 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_load_minimap_files.properPairs -rw-r--r-- root/root 38 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_load_minimap_insert_histogram.in -rw-r--r-- root/root 15 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_load_minimap_out_cluster2representative.in -rw-r--r-- root/root 20 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_load_minimap_out_cluster_counts.in -rw-r--r-- root/root 9 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_load_minimap_proper_pairs.in -rw-r--r-- root/root 778 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_1.fq -rw-r--r-- root/root 778 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_sam_pair_to_insert_reads_2.fq -rw-r--r-- root/root 2040 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa -rw-r--r-- root/root 896 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.sma -rw-r--r-- root/root 27900 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_sam_pair_to_insert_ref.fa.smi -rw-r--r-- root/root 33 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_catted_assembled_genes_fasta.expected.out.fa -rw-r--r-- root/root 33 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_catted_assemblies_fasta.expected.out.fa -rw-r--r-- root/root 27 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_gene_fa.db.fa -rw-r--r-- root/root 44 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_gene_fa.db.fa.fai -rw-r--r-- root/root 9 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_gene_fa.out.fa -rw-r--r-- root/root 551 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_mlst_reports.ariba.report.tsv -rw-r--r-- root/root 40 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_mlst_reports.mlst_profile.tsv -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_mlst_reports.out.details.tsv -rw-r--r-- root/root 21 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_mlst_reports.out.tsv -rw-r--r-- root/root 351 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_test_write_report.tsv -rw-r--r-- root/root 301 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_write_tb_resistance_calls_json.in.tsv -rw-r--r-- root/root 330 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/clusters_write_tb_resistance_calls_json.out.json -rw-r--r-- root/root 472 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/dummy.bam -rw-r--r-- root/root 32 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/faidx_test_write_fa_subset.in.fa -rw-r--r-- root/root 55 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/faidx_test_write_fa_subset.in.fa.fai -rw-r--r-- root/root 24 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/faidx_test_write_fa_subset.out.fa -rw-r--r-- root/root 589 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/graph_test_update_from_sam.bam -rw-r--r-- root/root 605 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/graph_test_update_from_sam.reads_1.fq -rw-r--r-- root/root 605 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/graph_test_update_from_sam.reads_2.fq -rw-r--r-- root/root 1036 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/graph_test_update_from_sam.ref.fa -rw-r--r-- root/root 36 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/graph_test_update_from_sam.ref.fa.fai -rw-r--r-- root/root 112 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/graph_test_write_all_links_to_file.out -rw-r--r-- root/root 376 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads.make_link.bam -rw-r--r-- root/root 176 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads.make_link.bam.bai -rw-r--r-- root/root 155 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads.make_link_1.fq -rw-r--r-- root/root 155 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads.make_link_2.fq -rw-r--r-- root/root 515 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads.no_link.bam -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads.no_link.bam.bai -rw-r--r-- root/root 450 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads.no_link_1.fq -rw-r--r-- root/root 450 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads.no_link_2.fq -rw-r--r-- root/root 605 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads_1.fq -rw-r--r-- root/root 605 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.reads_2.fq -rw-r--r-- root/root 1030 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.ref.fa -rw-r--r-- root/root 30 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/link_test_init.ref.fa.fai -rw-r--r-- root/root 413 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_bowtie2_reads_1.fq -rw-r--r-- root/root 413 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_bowtie2_reads_2.fq -rw-r--r-- root/root 199 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_bowtie2_ref.fa -rw-r--r-- root/root 16 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_bowtie2_ref.fa.fai -rw-r--r-- root/root 422 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads.bam -rw-r--r-- root/root 500 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_1.fq -rw-r--r-- root/root 464 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_bowtie2_remove_both_unmapped_reads_2.fq -rw-r--r-- root/root 639 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_bowtie2_sorted.bam -rw-r--r-- root/root 635 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_bowtie2_unsorted.bam -rw-r--r-- root/root 648 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_get_total_alignment_score.bam -rw-r--r-- root/root 643 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_sam_pair_to_insert.bam -rw-r--r-- root/root 360 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mapping_test_sam_to_fastq.bam -rw-r--r-- root/root 1328 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parse_extract_files_ok.zip -rw-r--r-- root/root 1116 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parse_extract_files_one_missing.zip -rw-r--r-- root/root 201 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parser_load_annotations.csv -rw-r--r-- root/root 227 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parser_load_header_mappings.tsv -rw-r--r-- root/root 238 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parser_write_files.expect.fa -rw-r--r-- root/root 405 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parser_write_files.expect.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parser_write_files/ -rw-r--r-- root/root 245 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parser_write_files/megares_annotations_v1.01.csv -rw-r--r-- root/root 219 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parser_write_files/megares_database_v1.01.fasta -rw-r--r-- root/root 279 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/megares_zip_parser_write_files/megares_to_external_header_mappings_v1.01.tsv -rw-r--r-- root/root 143 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_load_mic_file.tsv -rw-r--r-- root/root 450 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_load_summary_file.tsv -rw-r--r-- root/root 85 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv -rw-r--r-- root/root 74 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv -rw-r--r-- root/root 118 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv -rw-r--r-- root/root 107 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv -rw-r--r-- root/root 151 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv -rw-r--r-- root/root 128 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv -rw-r--r-- root/root 116 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv -rw-r--r-- root/root 116 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv -rw-r--r-- root/root 116 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv -rw-r--r-- root/root 106 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_profile_test.init.profile.tsv -rw-r--r-- root/root 164 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_profile_test.init_multiple_extra_columns.profile.tsv -rw-r--r-- root/root 90 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_profile_test.profile.tsv -rw-r--r-- root/root 551 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.all_present_perfect.report.in.tsv -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.details.tsv -rw-r--r-- root/root 21 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.all_present_perfect.report.out.tsv -rw-r--r-- root/root 573 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.het_snp.in.tsv -rw-r--r-- root/root 112 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.het_snp.out.details.tsv -rw-r--r-- root/root 23 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.het_snp.out.tsv -rw-r--r-- root/root 711 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.het_snps.in.tsv -rw-r--r-- root/root 120 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.het_snps.out.details.tsv -rw-r--r-- root/root 23 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.het_snps.out.tsv -rw-r--r-- root/root 555 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.new_st.report.in.tsv -rw-r--r-- root/root 106 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.new_st.report.out.details.tsv -rw-r--r-- root/root 27 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.new_st.report.out.tsv -rw-r--r-- root/root 439 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.one_gene_missing.in.tsv -rw-r--r-- root/root 94 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.one_gene_missing.out.details.tsv -rw-r--r-- root/root 23 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.one_gene_missing.out.tsv -rw-r--r-- root/root 40 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/mlst_reporter.profile.in.tsv -rw-r--r-- root/root 2428 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/pubmlst_getter.dbases.xml -rw-r--r-- root/root 32 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.expect.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/ -rw-r--r-- root/root 28 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene1.tfa -rw-r--r-- root/root 28 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/gene2.tfa -rw-r--r-- root/root 48 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/pubmlst_ref_prepare.test_load_fa_and_clusters.in/profile.txt -rw-r--r-- root/root 116 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/pubmlst_rename_seqs.expected.fa -rw-r--r-- root/root 116 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/pubmlst_rename_seqs.in.fa -rw-r--r-- root/root 596 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_cdhit_clstr_to_reads.in.clstr -rw-r--r-- root/root 967 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_test_run.expected.reads_1.fq -rw-r--r-- root/root 967 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_test_run.expected.reads_2.fq -rw-r--r-- root/root 6033 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_test_run.in.read_store -rw-r--r-- root/root 3086 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_test_run.in.reads_1.fq -rw-r--r-- root/root 3086 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_test_run.in.reads_2.fq -rw-r--r-- root/root 3060 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_test_run.in.ref.fa -rw-r--r-- root/root 1979 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_test_run_cdhit_est_2d.expected.clstr -rw-r--r-- root/root 3362 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_test_run_cdhit_est_2d.reads.in.fa -rw-r--r-- root/root 3060 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_filter_test_run_cdhit_est_2d.ref.in.fa -rw-r--r-- root/root 212 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_clean.in -rw-r--r-- root/root 212 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_compress_and_index_file.in -rw-r--r-- root/root 62 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_get_reads.expected.reads.fa -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_get_reads.expected.reads.fq -rw-r--r-- root/root 31 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fa -rw-r--r-- root/root 52 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_get_reads.expected.reads_1.fq -rw-r--r-- root/root 31 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fa -rw-r--r-- root/root 52 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_get_reads.expected.reads_2.fq -rw-r--r-- root/root 35 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.1.fq -rw-r--r-- root/root 35 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_get_reads.expected.reads_subset.2.fq -rw-r--r-- root/root 212 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_get_reads.in -rw-r--r-- root/root 212 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_sort_file.in -rw-r--r-- root/root 212 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/read_store_test_sort_file.out -rw-r--r-- root/root 58 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.in.fa -rw-r--r-- root/root 59 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_genes_getter.fix_virulencefinder_fasta_file.out.fa -rw-r--r-- root/root 102 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_fasta_to_metadata.coding.tsv -rw-r--r-- root/root 59 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_fasta_to_metadata.fa -rw-r--r-- root/root 102 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_fasta_to_metadata.noncoding.tsv -rw-r--r-- root/root 191 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.in.1.fa -rw-r--r-- root/root 117 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.in.1.tsv -rw-r--r-- root/root 231 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.in.2.fa -rw-r--r-- root/root 109 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.in.2.tsv -rw-r--r-- root/root 42 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.in.3.fa -rw-r--r-- root/root 315 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.in.4.fa -rw-r--r-- root/root 212 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.in.4.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/ -rw-r--r-- root/root 563 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/00.info.txt -rw-r--r-- root/root 174 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/00.version_info.txt -rw-r--r-- root/root 307 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_genes.log -rw-r--r-- root/root 97 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.log -rw-r--r-- root/root 192 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_metadata.tsv -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/01.filter.check_noncoding.log -rw-r--r-- root/root 422 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.all.fa -rw-r--r-- root/root 312 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.pickle -rw-r--r-- root/root 150 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.clusters.tsv -rw-r--r-- root/root 141 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.fa -rw-r--r-- root/root 50 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.gene.varonly.fa -rw-r--r-- root/root 231 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run.out/02.cdhit.noncoding.varonly.fa drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/ -rw-r--r-- root/root 218 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.auto_metadata.tsv -rw-r--r-- root/root 408 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.info.txt -rw-r--r-- root/root 174 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/00.version_info.txt -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_genes.log -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.log -rw-r--r-- root/root 218 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_metadata.tsv -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/01.filter.check_noncoding.log -rw-r--r-- root/root 464 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.all.fa -rw-r--r-- root/root 344 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.pickle -rw-r--r-- root/root 175 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.clusters.tsv -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.gene.varonly.fa -rw-r--r-- root/root 464 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_all_noncoding.out/02.cdhit.noncoding.varonly.fa drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/ -rw-r--r-- root/root 238 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.info.txt -rw-r--r-- root/root 156 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.rename_info -rw-r--r-- root/root 124 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/00.version_info.txt -rw-r--r-- root/root 208 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_genes.log -rw-r--r-- root/root 467 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.log -rw-r--r-- root/root 55 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_metadata.tsv -rw-r--r-- root/root 190 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/01.filter.check_noncoding.log -rw-r--r-- root/root 121 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.all.fa -rw-r--r-- root/root 72 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.pickle -rw-r--r-- root/root 20 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.clusters.tsv -rw-r--r-- root/root 100 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.gene.varonly.fa -rw-r--r-- root/root 21 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_preparer_test_run_noncoding_checks.out/02.cdhit.noncoding.varonly.fa -rw-r--r-- root/root 2575 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.allrefs.fa -rw-r--r-- root/root 2060 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.clusterrefs.fa -rw-r--r-- root/root 528 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_best_match_is_in_cluster.contigs.fa -rw-r--r-- root/root 2575 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.allrefs.fa -rw-r--r-- root/root 2060 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.clusterrefs.fa -rw-r--r-- root/root 528 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_best_match_not_in_cluster.contigs.fa -rw-r--r-- root/root 1795 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.all_refs.fa -rw-r--r-- root/root 1030 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.cluster_refs.fa -rw-r--r-- root/root 528 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_contained_ref_seq.contigs.fa -rw-r--r-- root/root 311 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.allrefs.fa -rw-r--r-- root/root 311 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.clusterrefs.fa -rw-r--r-- root/root 45 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_no_nucmer_match.contigs.fa -rw-r--r-- root/root 2575 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.allrefs.fa -rw-r--r-- root/root 1030 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.clusterrefs.fa -rw-r--r-- root/root 528 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_full_run_not_in_cluster.contigs.fa -rw-r--r-- root/root 271 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.coords -rw-r--r-- root/root 320 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ctg.fa -rw-r--r-- root/root 245 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.expect.fa -rw-r--r-- root/root 514 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_matching_contig_pieces.ref.fa -rw-r--r-- root/root 29 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_sequence_is_in_fasta_file.fa -rw-r--r-- root/root 1030 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_test_flanking.all_refs.fa -rw-r--r-- root/root 515 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_test_flanking.cluster_refs.fa -rw-r--r-- root/root 1224 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_test_flanking.contigs.fa -rw-r--r-- root/root 631 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/ref_seq_chooser_test_flanking.expected_contigs.fa -rw-r--r-- root/root 34 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_check_duplicate_name.fa -rw-r--r-- root/root 17 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_check_not_gene.fa -rw-r--r-- root/root 17 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_check_ok.fa -rw-r--r-- root/root 20 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_check_spaces_in_name.fa -rw-r--r-- root/root 17 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_check_too_long.fa -rw-r--r-- root/root 17 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_check_too_short.fa -rw-r--r-- root/root 224 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_fix_in.fa -rw-r--r-- root/root 143 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_fix_out.fa -rw-r--r-- root/root 130 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_fix_out.log -rw-r--r-- root/root 83 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_fix_out.removed.fa -rw-r--r-- root/root 78 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refcheck_test_fix_out.rename -rw-r--r-- root/root 4311 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref.in.fa -rw-r--r-- root/root 734 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref.in.tsv drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/ -rw-r--r-- root/root 113 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/00.info.txt -rw-r--r-- root/root 22 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/00.rename_info -rw-r--r-- root/root 1200 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/00.version_info.txt -rw-r--r-- root/root 318 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/01.filter.check_genes.log -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.log -rw-r--r-- root/root 734 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/01.filter.check_metadata.tsv -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/01.filter.check_noncoding.log -rw-r--r-- root/root 4311 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/02.cdhit.all.fa -rw-r--r-- root/root 314 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.pickle -rw-r--r-- root/root 121 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/02.cdhit.clusters.tsv -rw-r--r-- root/root 2544 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.fa -rw-r--r-- root/root 898 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/02.cdhit.gene.varonly.fa -rw-r--r-- root/root 669 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.fa -rw-r--r-- root/root 200 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/refdata_query_prepareref/02.cdhit.noncoding.varonly.fa -rw-r--r-- root/root 102 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.expect.clstrs.tsv -rw-r--r-- root/root 94 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.clstrs.tsv -rw-r--r-- root/root 820 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.fa -rw-r--r-- root/root 154 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_cluster_w_cdhit_clstrs_file.in.meta.tsv -rw-r--r-- root/root 106 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.expect.tsv -rw-r--r-- root/root 820 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.fa -rw-r--r-- root/root 154 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_cluster_w_cdhit_nocluster.in.tsv -rw-r--r-- root/root 154 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data.expected.all.fa -rw-r--r-- root/root 699 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.log -rw-r--r-- root/root 540 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data.expected.check_metadata.tsv -rw-r--r-- root/root 699 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data.expected.log -rw-r--r-- root/root 540 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data.expected.metadata.tsv -rw-r--r-- root/root 196 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data.in.fa -rw-r--r-- root/root 1047 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data_metadata.in.tsv -rw-r--r-- root/root 31 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data_non_coding.in.fa -rw-r--r-- root/root 93 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data_presence_absence.in.fa -rw-r--r-- root/root 118 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_filter_bad_data_variants_only.in.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_init_fails.empty.fa -rw-r--r-- root/root 0 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_init_fails.empty.tsv -rw-r--r-- root/root 43 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_init_fails.in.fa -rw-r--r-- root/root 57 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_init_ok.in.fa -rw-r--r-- root/root 111 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_init_ok.in.tsv -rw-r--r-- root/root 31 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_init_ok.params.json -rw-r--r-- root/root 42 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_init_ok.rename.tsv -rw-r--r-- root/root 11 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_keep_seqs_from_dict.fa -rw-r--r-- root/root 32 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_keep_seqs_from_dict.log -rw-r--r-- root/root 11 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_all_fasta_files.in.1 -rw-r--r-- root/root 11 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_all_fasta_files.in.2 -rw-r--r-- root/root 50 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_all_metadata_tsvs.1.tsv -rw-r--r-- root/root 89 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_all_metadata_tsvs.2.tsv -rw-r--r-- root/root 15 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_fasta_file.fa -rw-r--r-- root/root 25 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.1 -rw-r--r-- root/root 55 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_input_check_seq_names.bad.csv.2 -rw-r--r-- root/root 24 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.1 -rw-r--r-- root/root 11 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_input_check_seq_names.bad.fa.2 -rw-r--r-- root/root 25 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.1 -rw-r--r-- root/root 55 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_input_check_seq_names.good.csv.2 -rw-r--r-- root/root 11 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.1 -rw-r--r-- root/root 11 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_input_check_seq_names.good.fa.2 -rw-r--r-- root/root 139 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_metadata_tsv.tsv -rw-r--r-- root/root 34 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_load_rename_file.tsv -rw-r--r-- root/root 193 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_remove_bad_genes.in.fa -rw-r--r-- root/root 86 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_remove_bad_genes.in.tsv -rw-r--r-- root/root 235 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_remove_bad_noncoding.in.fa -rw-r--r-- root/root 105 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_remove_bad_noncoding.in.tsv -rw-r--r-- root/root 178 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_rename_sequences.fa -rw-r--r-- root/root 431 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_rename_sequences_metadata.tsv -rw-r--r-- root/root 28 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_sequence.in.fa -rw-r--r-- root/root 34 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_sequence.in.tsv -rw-r--r-- root/root 72 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_sequence_type.in.fa -rw-r--r-- root/root 88 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_sequence_type.in.tsv -rw-r--r-- root/root 109 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_all_non_wild_type_variants.ref.fa -rw-r--r-- root/root 395 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_all_non_wild_type_variants.tsv -rw-r--r-- root/root 89 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_cluster_with_cdhit.expected.clusters.tsv -rw-r--r-- root/root 604 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.fa -rw-r--r-- root/root 133 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_cluster_with_cdhit.in.tsv -rw-r--r-- root/root 285 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_remove_bad_genes.log -rw-r--r-- root/root 79 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_remove_bad_noncoding.log -rw-r--r-- root/root 126 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_rename_sequences.out -rw-r--r-- root/root 88 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_write_cluster_allocation_file.expected -rw-r--r-- root/root 84 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_write_seqs_to_fasta.expected.fa -rw-r--r-- root/root 140 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.fa -rw-r--r-- root/root 75 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_test_write_seqs_to_fasta.in.tsv -rw-r--r-- root/root 89 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_write_metadata_tsv.expected.tsv -rw-r--r-- root/root 89 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_write_metadata_tsv.tsv -rw-r--r-- root/root 64 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_write_sequences_to_files.all.fa -rw-r--r-- root/root 13 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_write_sequences_to_files.gene.fa -rw-r--r-- root/root 14 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_write_sequences_to_files.gene.varonly.fa -rw-r--r-- root/root 25 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.fa -rw-r--r-- root/root 12 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/reference_data_write_sequences_to_files.noncoding.varonly.fa -rw-r--r-- root/root 832 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/report_filter_test_init_bad.tsv -rw-r--r-- root/root 1004 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/report_filter_test_init_good.tsv -rw-r--r-- root/root 832 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/report_filter_test_load_report_bad.tsv -rw-r--r-- root/root 1004 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/report_filter_test_load_report_good.tsv -rw-r--r-- root/root 1112 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/report_filter_test_run.expected.tsv -rw-r--r-- root/root 1649 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/report_filter_test_run.in.tsv -rw-r--r-- root/root 836 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/report_filter_test_write_report.tsv -rw-r--r-- root/root 51 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/report_flag_expander.run.in.tsv -rw-r--r-- root/root 120 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/report_flag_expander.run.out.tsv -rw-r--r-- root/root 1029 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa -rw-r--r-- root/root 36 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.asmbly.fa.fai -rw-r--r-- root/root 22642 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.bam -rw-r--r-- root/root 22 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.cov -rw-r--r-- root/root 4786 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.depths.gz -rw-r--r-- root/root 932 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.expect.vcf -rw-r--r-- root/root 8232 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.for_reads.fa -rw-r--r-- root/root 232153 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_1.fq -rw-r--r-- root/root 232153 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_make_vcf_and_depths_files.reads_2.fq -rw-r--r-- root/root 4744 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_get_depths_at_position.bam -rw-r--r-- root/root 1022 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa -rw-r--r-- root/root 17 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_get_depths_at_position.ref.fa.fai -rw-r--r-- root/root 128 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_get_read_depths.gz -rw-r--r-- root/root 89 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_get_read_depths.gz.tbi -rw-r--r-- root/root 4144 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_get_variant_positions_from_vcf.vcf -rw-r--r-- root/root 10132 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz -rw-r--r-- root/root 210 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_get_variants.read_depths.gz.tbi -rw-r--r-- root/root 4144 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_get_variants.vcf -rw-r--r-- root/root 24 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_total_depth_per_contig -rw-r--r-- root/root 3853 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/samtools_variants_test_variants_in_coords.vcf -rw-r--r-- root/root 1677 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv -rw-r--r-- root/root 1524 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_gather_unfiltered_output_data.in.2.tsv -rw-r--r-- root/root 1903 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_sample_test_column_names_tuples_and_het_snps.tsv -rw-r--r-- root/root 1902 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_sample_test_column_summary_data.tsv -rw-r--r-- root/root 1720 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_sample_test_load_file.in.tsv -rw-r--r-- root/root 1801 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_sample_test_non_synon_variants.tsv -rw-r--r-- root/root 1728 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_sample_test_var_groups.tsv -rw-r--r-- root/root 12 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_test_init.fofn -rw-r--r-- root/root 104 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_test_load_fofn -rw-r--r-- root/root 886 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_test_load_input_files.1.tsv -rw-r--r-- root/root 1227 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_test_load_input_files.2.tsv -rw-r--r-- root/root 55 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_test_newick_from_dist_matrix.distances -rw-r--r-- root/root 3658 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_test_whole_run.in.1.tsv -rw-r--r-- root/root 1660 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_test_whole_run.in.2.tsv -rw-r--r-- root/root 3349 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_test_whole_run.out.csv -rw-r--r-- root/root 55 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_test_write_distance_matrix.distances -rw-r--r-- root/root 1451 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_to_matrix.1.tsv -rw-r--r-- root/root 1524 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/summary_to_matrix.2.tsv -rw-r--r-- root/root 705 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/tb_genbank_to_gene_coords.gb -rw-r--r-- root/root 382 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/tb_report_to_resistance_dict.tsv -rw-r--r-- root/root 217 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/tb_write_prepareref_metadata_file.tsv -rw-r--r-- root/root 24 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/test_common_cat_files.in.1 -rw-r--r-- root/root 36 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/test_common_cat_files.in.2 -rw-r--r-- root/root 12 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/test_common_cat_files.in.3 -rw-r--r-- root/root 72 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/test_common_cat_files.out -rw-r--r-- root/root 163 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/vfdb_parser_test_run.in.fa -rw-r--r-- root/root 95 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/vfdb_parser_test_run.out.fa -rw-r--r-- root/root 291 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/data/vfdb_parser_test_run.out.tsv -rw-r--r-- root/root 236 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/external_progs_test.py -rw-r--r-- root/root 732 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/faidx_test.py -rw-r--r-- root/root 2109 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/flag_test.py -rw-r--r-- root/root 1500 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/histogram_test.py -rw-r--r-- root/root 5941 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/link_test.py -rw-r--r-- root/root 5811 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/mapping_test.py -rw-r--r-- root/root 1379 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/megares_data_finder_test.py -rw-r--r-- root/root 4211 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/megares_zip_parser_test.py -rw-r--r-- root/root 14919 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/mic_plotter_test.py -rw-r--r-- root/root 2587 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/mlst_profile_test.py -rw-r--r-- root/root 4757 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/mlst_reporter_test.py -rw-r--r-- root/root 529 2022-03-16 19:20 ./usr/lib/python3/dist-packages/ariba/tests/ncbi_getter_test.py -rw-r--r-- root/root 2112 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/pubmlst_getter_test.py -rw-r--r-- root/root 2355 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/pubmlst_ref_preparer_test.py -rw-r--r-- root/root 2688 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/read_filter_test.py -rw-r--r-- root/root 5944 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/read_store_test.py -rw-r--r-- root/root 836 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/ref_genes_getter_test.py -rw-r--r-- root/root 7897 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/ref_preparer_test.py -rw-r--r-- root/root 6631 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/ref_seq_chooser_test.py -rw-r--r-- root/root 32281 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/reference_data_test.py -rw-r--r-- root/root 20926 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/report_filter_test.py -rw-r--r-- root/root 715 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/report_flag_expander_test.py -rw-r--r-- root/root 6793 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/samtools_variants_test.py -rw-r--r-- root/root 4716 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/scaffold_graph_test.py -rw-r--r-- root/root 3323 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/sequence_metadata_test.py -rw-r--r-- root/root 3312 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/sequence_variant_test.py -rw-r--r-- root/root 39403 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/summary_cluster_test.py -rw-r--r-- root/root 10823 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/summary_cluster_variant_test.py -rw-r--r-- root/root 4521 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/summary_sample_test.py -rw-r--r-- root/root 33085 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/summary_test.py -rw-r--r-- root/root 6244 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/tb_test.py -rw-r--r-- root/root 3798 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/test_refdata_query.py -rw-r--r-- root/root 197 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/versions_test.py -rw-r--r-- root/root 2562 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/tests/vfdb_parser_test.py -rw-r--r-- root/root 2213 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/versions.py -rw-r--r-- root/root 1609 2020-09-07 12:37 ./usr/lib/python3/dist-packages/ariba/vfdb_parser.py -rw-r--r-- root/root 19096 2022-03-16 19:20 ./usr/lib/python3/dist-packages/fermilite_ariba.cpython-310-riscv64-linux-gnu.so -rw-r--r-- root/root 48088 2022-03-16 19:20 ./usr/lib/python3/dist-packages/minimap_ariba.cpython-310-riscv64-linux-gnu.so -rw-r--r-- root/root 31568 2022-03-16 19:20 ./usr/lib/python3/dist-packages/vcfcall_ariba.cpython-310-riscv64-linux-gnu.so drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/share/ drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/share/doc/ariba/ -rw-r--r-- root/root 847 2022-03-16 19:20 ./usr/share/doc/ariba/changelog.Debian.gz -rw-r--r-- root/root 1160 2021-12-18 18:08 ./usr/share/doc/ariba/copyright drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/share/man/ drwxr-xr-x root/root 0 2022-03-16 19:20 ./usr/share/man/man1/ -rw-r--r-- root/root 1053 2022-03-16 19:20 ./usr/share/man/man1/ariba.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: riscv64 Build Type: any Build-Space: 76492 Build-Time: 618 Distribution: jammy-proposed Host Architecture: riscv64 Install-Time: 1146 Job: ariba_2.14.6+ds-3build1.dsc Machine Architecture: riscv64 Package: ariba Package-Time: 1799 Source-Version: 2.14.6+ds-3build1 Space: 76492 Status: successful Version: 2.14.6+ds-3build1 -------------------------------------------------------------------------------- Finished at 2022-03-17T17:52:51Z Build needed 00:29:59, 76492k disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23248863 Scanning for processes to kill in build PACKAGEBUILD-23248863 RUN: /usr/share/launchpad-buildd/bin/in-target umount-chroot --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23248863 Stopping target for build PACKAGEBUILD-23248863 RUN: /usr/share/launchpad-buildd/bin/in-target remove-build --backend=chroot --series=jammy --arch=riscv64 PACKAGEBUILD-23248863 Removing build PACKAGEBUILD-23248863