sbuild (Debian sbuild) 0.91.10 (27 June 2026) on carme.larted.org.uk +==============================================================================+ | cct 1:1.0.3-1 (amd64) Thu, 09 Jul 2026 04:48:32 +0000 | +==============================================================================+ Package: cct Version: 1:1.0.3-1 Source Version: 1:1.0.3-1 Distribution: perl-5.44-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Thu, 09 Jul 2026 04:48:34 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup cct_1.0.3-1 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup cct_1.0.3-1 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Thu, 09 Jul 2026 04:48:34 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Hit:2 http://deb.debian.org/debian unstable InRelease Hit:3 http://deb.debian.org/debian sid InRelease Get:1 file:/srv/reprepro perl-5.44 InRelease [3039 B] Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Thu, 09 Jul 2026 04:48:36 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/cct_1.0.3-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Thu, 09 Jul 2026 04:48:37 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), debhelper, build-essential Filtered Build-Depends: debhelper-compat (= 13), debhelper, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/cct-04sq6m/resolver-n5EBks/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/cct-04sq6m/resolver-n5EBks/apt_archive ./ InRelease Get:2 copy:/build/cct-04sq6m/resolver-n5EBks/apt_archive ./ Release [609 B] Ign:3 copy:/build/cct-04sq6m/resolver-n5EBks/apt_archive ./ Release.gpg Get:4 copy:/build/cct-04sq6m/resolver-n5EBks/apt_archive ./ Sources [611 B] Get:5 copy:/build/cct-04sq6m/resolver-n5EBks/apt_archive ./ Packages [650 B] Fetched 1870 B in 0s (178 kB/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... Solving dependencies... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2-16 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx python3:any libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2-16 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 11.9 MB of archives. After this operation, 54.3 MB of additional disk space will be used. Get:1 copy:/build/cct-04sq6m/resolver-n5EBks/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [856 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.47-4 [345 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.47-4 [111 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.47-4 [43.0 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 1.0-3 [332 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2+b2 [69.0 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.24.1-1 [1336 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.42.2-1 [100.0 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-3 [49.2 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.21-1 [332 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.73-2 [516 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1+nmu1 [60.0 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.18.1-4 [877 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 1.0-3 [820 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 14.3 [77.3 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-11 [539 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 22 [12.2 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.1-1 [17.1 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.1-1 [6020 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.195-1 [58.1 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-4 [108 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.15.3+dfsg-1 [642 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 1.0-3 [2658 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.22 [216 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 debhelper all 14.3 [934 kB] Preconfiguring packages ... Fetched 11.9 MB in 0s (148 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 14518 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.47-4_amd64.deb ... Unpacking libmagic-mgc (1:5.47-4) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.47-4_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.47-4) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.47-4_amd64.deb ... Unpacking file (1:5.47-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_1.0-3_amd64.deb ... Unpacking gettext-base (1.0-3) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-2+b2_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-2+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../06-groff-base_1.24.1-1_amd64.deb ... Unpacking groff-base (1.24.1-1) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../07-bsdextrautils_2.42.2-1_amd64.deb ... Unpacking bsdextrautils (2.42.2-1) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../08-libpipeline1_1.5.8-3_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-3) ... Selecting previously unselected package man-db. Preparing to unpack .../09-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../10-m4_1.4.21-1_amd64.deb ... Unpacking m4 (1.4.21-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../11-autoconf_2.73-2_all.deb ... Unpacking autoconf (2.73-2) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../12-autotools-dev_20240727.1+nmu1_all.deb ... Unpacking autotools-dev (20240727.1+nmu1) ... Selecting previously unselected package automake. Preparing to unpack .../13-automake_1%3a1.18.1-4_all.deb ... Unpacking automake (1:1.18.1-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../14-autopoint_1.0-3_all.deb ... Unpacking autopoint (1.0-3) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../15-libdebhelper-perl_14.3_all.deb ... Unpacking libdebhelper-perl (14.3) ... Selecting previously unselected package libtool. Preparing to unpack .../16-libtool_2.5.4-11_all.deb ... Unpacking libtool (2.5.4-11) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../17-dh-autoreconf_22_all.deb ... Unpacking dh-autoreconf (22) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../18-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../19-libfile-stripnondeterminism-perl_1.15.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../20-dh-strip-nondeterminism_1.15.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.1-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../21-libelf1t64_0.195-1_amd64.deb ... Unpacking libelf1t64:amd64 (0.195-1) ... Selecting previously unselected package dwz. Preparing to unpack .../22-dwz_0.16-4_amd64.deb ... Unpacking dwz (0.16-4) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../23-libxml2-16_2.15.3+dfsg-1_amd64.deb ... Unpacking libxml2-16:amd64 (2.15.3+dfsg-1) ... Selecting previously unselected package gettext. Preparing to unpack .../24-gettext_1.0-3_amd64.deb ... Unpacking gettext (1.0-3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../25-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../26-po-debconf_1.0.22_all.deb ... Unpacking po-debconf (1.0.22) ... Selecting previously unselected package debhelper. Preparing to unpack .../27-debhelper_14.3_all.deb ... Unpacking debhelper (14.3) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../28-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.8-3) ... Setting up bsdextrautils (2.42.2-1) ... Setting up libmagic-mgc (1:5.47-4) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.15.3+dfsg-1) ... Setting up libdebhelper-perl (14.3) ... Setting up libmagic1t64:amd64 (1:5.47-4) ... Setting up gettext-base (1.0-3) ... Setting up m4 (1.4.21-1) ... Setting up file (1:5.47-4) ... Setting up libelf1t64:amd64 (0.195-1) ... Setting up autotools-dev (20240727.1+nmu1) ... Setting up autopoint (1.0-3) ... Setting up autoconf (2.73-2) ... Setting up dwz (0.16-4) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2+b2) ... Setting up automake (1:1.18.1-4) ... update-alternatives: using /usr/bin/automake-1.18 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.1-1) ... Setting up gettext (1.0-3) ... Setting up libtool (2.5.4-11) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (22) ... Setting up dh-strip-nondeterminism (1.15.1-1) ... Setting up groff-base (1.24.1-1) ... Setting up po-debconf (1.0.22) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (14.3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.42-17) ... +------------------------------------------------------------------------------+ | Check architectures Thu, 09 Jul 2026 04:48:43 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment Thu, 09 Jul 2026 04:48:43 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 7.0.10+deb14-amd64 #1 SMP PREEMPT_DYNAMIC Debian 7.0.10-1 (2026-05-27) amd64 (x86_64) Toolchain package versions: binutils_2.46.50.20260617-1 dpkg-dev_1.23.7 g++-15_15.3.0-1 gcc-15_15.3.0-1 libc6-dev_2.42-17 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 linux-libc-dev_7.1.3-1 Package versions: apt_3.3.1 autoconf_2.73-2 automake_1:1.18.1-4 autopoint_1.0-3 autotools-dev_20240727.1+nmu1 base-files_14.2 base-passwd_3.6.8 bash_5.3-3 binutils_2.46.50.20260617-1 binutils-common_2.46.50.20260617-1 binutils-x86-64-linux-gnu_2.46.50.20260617-1 bsdextrautils_2.42.2-1 build-essential_12.12 bzip2_1.0.8-6+b2 coreutils_9.10-1 cpp_4:15.2.0-5+b1 cpp-15_15.3.0-1 cpp-15-x86-64-linux-gnu_15.3.0-1 cpp-x86-64-linux-gnu_4:15.2.0-5+b1 dash_0.5.12-12 debconf_1.5.92 debhelper_14.3 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_22 dh-strip-nondeterminism_1.15.1-1 diffutils_1:3.12-1 dirmngr_2.4.9-5 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-4 eatmydata_131-2 file_1:5.47-4 findutils_4.10.0-4 g++_4:15.2.0-5+b1 g++-15_15.3.0-1 g++-15-x86-64-linux-gnu_15.3.0-1 g++-x86-64-linux-gnu_4:15.2.0-5+b1 gcc_4:15.2.0-5+b1 gcc-15_15.3.0-1 gcc-15-base_15.3.0-1 gcc-15-x86-64-linux-gnu_15.3.0-1 gcc-16-base_16.1.0-2 gcc-x86-64-linux-gnu_4:15.2.0-5+b1 gettext_1.0-3 gettext-base_1.0-3 gnupg_2.4.9-5 gnupg-l10n_2.4.9-5 gpg_2.4.9-5 gpg-agent_2.4.9-5 gpgconf_2.4.9-5 gpgsm_2.4.9-5 grep_3.12-1 groff-base_1.24.1-1 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.4.0-1 libapt-pkg7.0_3.3.1 libarchive-zip-perl_1.68-1 libasan8_16.1.0-2 libassuan9_3.0.2-2+b2 libatomic1_16.1.0-2 libattr1_1:2.6.0-1 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46.50.20260617-1 libblkid1_2.42.2-1 libbz2-1.0_1.0.8-6+b2 libc-bin_2.42-17 libc-dev-bin_2.42-17 libc-gconv-modules-extra_2.42-17 libc6_2.42-17 libc6-dev_2.42-17 libcap-ng0_0.9.3-1+b1 libcc1-0_16.1.0-2 libcrypt1_1:4.5.1-1+b1 libctf-nobfd0_2.46.50.20260617-1 libctf0_2.46.50.20260617-1 libdb5.3t64_5.3.28+dfsg2-11+b1 libdebconfclient0_0.283 libdebhelper-perl_14.3 libdpkg-perl_1.23.7 libeatmydata1_131-2+b2 libelf1t64_0.195-1 libffi8_3.5.2-4 libfile-stripnondeterminism-perl_1.15.1-1 libgcc-15-dev_15.3.0-1 libgcc-s1_16.1.0-2 libgcrypt20_1.12.2-1 libgdbm-compat4t64_1.26-1+b2 libgdbm6t64_1.26-1+b2 libgmp10_2:6.3.0+dfsg-5+b2 libgnutls30t64_3.8.13-1 libgomp1_16.1.0-2 libgpg-error0_1.61-3 libgprofng0_2.46.50.20260617-1 libhogweed6t64_3.10.2-1+b1 libhwasan0_16.1.0-2 libidn2-0_2.3.8-5 libisl23_0.27-2 libitm1_16.1.0-2 libjansson4_2.15.1-1 libksba8_1.8.0-3 libldap2_2.6.13+dfsg-1+b1 liblsan0_16.1.0-2 liblz4-1_1.10.0-10 liblzma5_5.8.3-1 libmagic-mgc_1:5.47-4 libmagic1t64_1:5.47-4 libmd0_1.2.0-2 libmount1_2.42.2-1 libmpc3_1.3.1-3 libmpfr6_4.2.2-3 libncursesw6_6.6+20260608-2 libnettle8t64_3.10.2-1+b1 libnpth0t64_1.8-3+b2 libp11-kit0_0.26.2-3 libpam-modules_1.7.0-8 libpam-modules-bin_1.7.0-8 libpam-runtime_1.7.0-8 libpam0g_1.7.0-8 libpcre2-8-0_10.46-1+b2 libperl5.40_5.40.1-8 libperl5.44_5.44.0~rc2-1 libpipeline1_1.5.8-3 libquadmath0_16.1.0-2 libreadline8t64_8.3-4 libsasl2-2_2.1.28+dfsg1-11 libsasl2-modules-db_2.1.28+dfsg1-11 libseccomp2_2.6.0-2+b1 libselinux1_3.10-1 libsframe3_2.46.50.20260617-1 libsmartcols1_2.42.2-1 libsqlite3-0_3.53.3-1 libssl3t64_3.6.3-1 libstdc++-15-dev_15.3.0-1 libstdc++6_16.1.0-2 libsystemd0_261.1-2 libtasn1-6_4.21.0-2+b1 libtinfo6_6.6+20260608-2 libtool_2.5.4-11 libtsan2_16.1.0-2 libubsan1_16.1.0-2 libuchardet0_0.0.8-2+b2 libudev1_261.1-2 libunistring5_1.4.2-1 libuuid1_2.42.2-1 libxml2-16_2.15.3+dfsg-1 libxxhash0_0.8.3-2+b2 libzstd1_1.5.7+dfsg-3+b2 linux-libc-dev_7.1.3-1 m4_1.4.21-1 make_4.4.1-3 man-db_2.13.1-1 mawk_1.3.4.20260302-1 ncurses-base_6.6+20260608-2 ncurses-bin_6.6+20260608-2 openssl-provider-legacy_3.6.3-1 patch_2.8-2 perl_5.44.0~rc2-1 perl-base_5.44.0~rc2-1 perl-modules-5.40_5.40.1-8 perl-modules-5.44_5.44.0~rc2-1 pinentry-curses_1.3.2-4 po-debconf_1.0.22 readline-common_8.3-4 rpcsvc-proto_1.4.4-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-3 sensible-utils_0.0.26 sqv_1.4.0-1 sysvinit-utils_3.18-1 tar_1.35+dfsg-4 util-linux_2.42.2-1 xz-utils_5.8.3-1 zlib1g_1:1.3.dfsg+really1.3.2-3 +------------------------------------------------------------------------------+ | Build Thu, 09 Jul 2026 04:48:43 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: cct Binary: cct, cct-examples Architecture: all Version: 1:1.0.3-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://stothard.afns.ualberta.ca/downloads/CCT/ Standards-Version: 4.6.0 Vcs-Browser: https://salsa.debian.org/med-team/cct Vcs-Git: https://salsa.debian.org/med-team/cct.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), debhelper Package-List: cct deb science optional arch=all cct-examples deb science optional arch=all Checksums-Sha1: 588f561c9cc4faaad979fbf1c225b681d5f978e0 81734736 cct_1.0.3.orig.tar.xz 06ace14e2579172379e7318292881d5a2ca8af49 11652 cct_1.0.3-1.debian.tar.xz Checksums-Sha256: e0f4d56ccf25843530e9386b2daab97ea02bd00b60df348082be3b921dd8edc7 81734736 cct_1.0.3.orig.tar.xz c04e1b0c8f90dbec3a39d0551f4e45ffd07809d1feb04fee0818c7ae204c6159 11652 cct_1.0.3-1.debian.tar.xz Files: 8d4d1b9f70e70a6d01e3d8d8b90c8eda 81734736 cct_1.0.3.orig.tar.xz 3f88301874c53e545f9585c61dd1dcd9 11652 cct_1.0.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmHkNZYRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtEJLA/+LLgT+bQwoSPjRyaAwhB7F4X2NFCZlp7+ D3l1ruKpT5oJXjpORgW4cknpOuaVH+VvZLxCMMNb9/E231ZqvahFOKf1sC0Xv4KN v5UkVaFEmHOKhAnJKwEGhBgha9hnG9i17d9HAJ7hyZ3f/CILAZMjVR1btmjUwK26 Qev/j+J5fn5YHaS2U/iN9M38xD+It0kQKfKpgbapHJAmwwazhNLJIVDPmWNn4uE2 5SLLI+Vd5hll5MqT0uuMCcLDq3EYrNMAsso8I29aR7i39QmgrU1FDvQDQpi7Vd7c mzgJwVFoCEM22qxyysniNbejffYinSuajOs/OULGmN0dJi/FhM7cNAVqb+Ftf13q ihqogWXfF7x0Sbf44RT6ZFbxrXSrK1FnimyLj/8TgHh15oKclU+lRBH9/mr4x9Qa aYPATTVw0SdkpFjEBC/990AZHZtvjHIaWOI0s8eM/78tD+HSIKPDXVuDHCeYxQfm kwP0YWg3lL9uBtZD1OJODAKFAJI9V+ptv3vJwZvUo/R7JzatsUVZCwN73MCdX40I Z+62PqMZvrnqoAQAiv5zN/oBgL4w5YNKwTvpc+qd6NOxIdgbmxpt51fa2rUMVrpL jMH+wwOG0xBrsdSX4DOKDd3n1XqiEm/hHe1WEgRii+ZBrVIpyR2p9TAifIc8rguo vWFXn0Ljm4Q= =Vczx -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./cct_1.0.3-1.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./cct_1.0.3-1.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting cct in /build/cct-04sq6m/cct-1.0.3 dpkg-source: info: unpacking cct_1.0.3.orig.tar.xz dpkg-source: info: unpacking cct_1.0.3-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying cgview_path.patch dpkg-source: info: applying testscripts.patch dpkg-source: info: applying fix_cgview_path.patch clean up apt cache ------------------ Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Time Build Commands Thu, 09 Jul 2026 04:48:47 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network cct_1.0.3-1 perl-5.44-throwaway amd64 ------------------------------------------------------------------------------------------------------------ I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network cct_1.0.3-1 perl-5.44-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/cct-04sq6m/cct-1.0.3 SCHROOT_ALIAS_NAME=perl-5.44-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.44-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.44-amd64-debomatic-7aead9c0-8c7c-40f9-8cdd-c265e4e9b1c6 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package cct dpkg-buildpackage: info: source version 1:1.0.3-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building cct using existing ../cct_1.0.3.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building cct in ../cct_1.0.3-1.debian.tar.xz dpkg-source: info: building cct in ../cct_1.0.3-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep debian/rules override_dh_install make[1]: Entering directory '/build/cct-04sq6m/cct-1.0.3' dh_install mkdir -p debian/cct/usr/bin for scr in debian/cct/usr/share/cct/scripts/*.sh ; do \ binscr=`basename ${scr} .sh` ; \ ln -s /usr/share/cct/scripts/generic debian/cct/usr/bin/${binscr} ; \ done for scr in debian/cct/usr/share/cct/scripts/*.pl ; do \ binscr=`basename ${scr} .pl` ; \ ln -s /usr/share/cct/scripts/generic debian/cct/usr/bin/${binscr} ; \ done ln -s /etc/cct debian/cct/usr/share/cct/conf # Move "hidden" examples into example package for sample in `find debian -type d \( -name "sample_output" -o -name "test_input" \)` ; do \ base=`dirname ${sample} | sed 's#debian/cct#debian/cct-examples#'` ; \ mkdir -p ${base} ; \ mv ${sample} ${base} ; \ done for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \ sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \ done grep: debian/cct/usr/bin/fetch_all_refseq_chloroplast_genomes: No such file or directory grep: debian/cct/usr/bin/create_zoomed_maps: No such file or directory grep: debian/cct/usr/bin/fetch_refseq_bacterial_genomes_by_name: No such file or directory grep: debian/cct/usr/bin/build_blast_atlas: No such file or directory grep: debian/cct/usr/bin/cgview_comparison_tool: No such file or directory grep: debian/cct/usr/bin/build_blast_atlas_all_vs_all: No such file or directory grep: debian/cct/usr/bin/fetch_all_refseq_bacterial_genomes: No such file or directory grep: debian/cct/usr/bin/fetch_genome_by_accession: No such file or directory grep: debian/cct/usr/bin/redraw_maps: No such file or directory grep: debian/cct/usr/bin/process_test_projects: No such file or directory grep: debian/cct/usr/bin/process_sample_projects: No such file or directory grep: debian/cct/usr/bin/remove_long_seqs: No such file or directory grep: debian/cct/usr/bin/ncbi_search: No such file or directory grep: debian/cct/usr/bin/convert_vcf_to_features: No such file or directory grep: debian/cct/usr/bin/check_env: No such file or directory grep: debian/cct/usr/bin/fetch_all_refseq_mitochondrial_genomes: No such file or directory grep: debian/cct/usr/bin/build_cog_db: No such file or directory grep: debian/cct/usr/bin/remove_short_seqs: No such file or directory grep: debian/cct/usr/share/cct/conf: No such file or directory make[1]: Leaving directory '/build/cct-04sq6m/cct-1.0.3' dh_installdocs dh_installchangelogs dh_installman dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_installdeb dh_gencontrol dpkg-gencontrol: warning: Depends field of package cct-examples: substitution variable ${perl:Depends} used, but is not defined dh_md5sums dh_builddeb dpkg-deb: building package 'cct' in '../cct_1.0.3-1_all.deb'. dpkg-deb: building package 'cct-examples' in '../cct-examples_1.0.3-1_all.deb'. dpkg-genbuildinfo -O../cct_1.0.3-1_amd64.buildinfo dpkg-genchanges -O../cct_1.0.3-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2026-07-09T04:50:59Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Thu, 09 Jul 2026 04:51:00 +0000 | +------------------------------------------------------------------------------+ cct_1.0.3-1_amd64.changes: -------------------------- Format: 1.8 Date: Sun, 16 Jan 2022 14:49:39 +0100 Source: cct Binary: cct cct-examples Architecture: source all Version: 1:1.0.3-1 Distribution: perl-5.44-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: cct - visually comparing bacterial, plasmid, chloroplast, or mitochondr cct-examples - example data for testing the package cct Changes: cct (1:1.0.3-1) unstable; urgency=medium . * New upstream version * Standards-Version: 4.6.0 (routine-update) * Add missing build dependency on dh addon. Checksums-Sha1: 15d1468df2f30f1233b538b585d7fa3e30104372 1089 cct_1.0.3-1.dsc 588f561c9cc4faaad979fbf1c225b681d5f978e0 81734736 cct_1.0.3.orig.tar.xz f873ebff105a84fc48fe6e609feb2189ba3137cc 11660 cct_1.0.3-1.debian.tar.xz fb02cca4a44cf48793ffadb379097632ae81ba69 41893488 cct-examples_1.0.3-1_all.deb 143391d6994b1fa548cc05807c142cdaee146ddf 36332512 cct_1.0.3-1_all.deb c4b85b914df0972da23e81c8312ac6f4b5fefe2e 5115 cct_1.0.3-1_amd64.buildinfo Checksums-Sha256: 0eb3cb1bc37bd281c75f81029e78f9cbd6a083280f204788fe4d5810cbfcb8da 1089 cct_1.0.3-1.dsc e0f4d56ccf25843530e9386b2daab97ea02bd00b60df348082be3b921dd8edc7 81734736 cct_1.0.3.orig.tar.xz d5a49eb742a9439e5dded2fe026a908c35d1eb6df1e3d4ee07e92f4c3ce804b3 11660 cct_1.0.3-1.debian.tar.xz ed7fc604561feed4024e469656442cae04be8a8c31005219cb8cc7214056d5ef 41893488 cct-examples_1.0.3-1_all.deb 476385e26e2ef7d463c609afec92f4f78af7e250dc5e3fb386e087302942e1c4 36332512 cct_1.0.3-1_all.deb faa54f4372362363e920432e287517790930bbe56284ad5e18cdc754ef1c90f1 5115 cct_1.0.3-1_amd64.buildinfo Files: a611d387bd4a9a0f28326ed87b9a2f3a 1089 science optional cct_1.0.3-1.dsc 8d4d1b9f70e70a6d01e3d8d8b90c8eda 81734736 science optional cct_1.0.3.orig.tar.xz 940baee815d36e6c9cdbea8601766c4c 11660 science optional cct_1.0.3-1.debian.tar.xz be2fe5ca9d4defcf5aefb63ab4f7c399 41893488 science optional cct-examples_1.0.3-1_all.deb f05c6d934fb7cccf8a4847994ccf409d 36332512 science optional cct_1.0.3-1_all.deb aafd34a9b3b17bcbf6a0eac4809905d4 5115 science optional cct_1.0.3-1_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo Thu, 09 Jul 2026 04:51:00 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: cct Binary: cct cct-examples Architecture: all source Version: 1:1.0.3-1 Checksums-Md5: a611d387bd4a9a0f28326ed87b9a2f3a 1089 cct_1.0.3-1.dsc be2fe5ca9d4defcf5aefb63ab4f7c399 41893488 cct-examples_1.0.3-1_all.deb f05c6d934fb7cccf8a4847994ccf409d 36332512 cct_1.0.3-1_all.deb Checksums-Sha1: 15d1468df2f30f1233b538b585d7fa3e30104372 1089 cct_1.0.3-1.dsc fb02cca4a44cf48793ffadb379097632ae81ba69 41893488 cct-examples_1.0.3-1_all.deb 143391d6994b1fa548cc05807c142cdaee146ddf 36332512 cct_1.0.3-1_all.deb Checksums-Sha256: 0eb3cb1bc37bd281c75f81029e78f9cbd6a083280f204788fe4d5810cbfcb8da 1089 cct_1.0.3-1.dsc ed7fc604561feed4024e469656442cae04be8a8c31005219cb8cc7214056d5ef 41893488 cct-examples_1.0.3-1_all.deb 476385e26e2ef7d463c609afec92f4f78af7e250dc5e3fb386e087302942e1c4 36332512 cct_1.0.3-1_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Thu, 09 Jul 2026 04:50:58 +0000 Build-Path: /build/cct-04sq6m/cct-1.0.3 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.73-2), automake (= 1:1.18.1-4), autopoint (= 1.0-3), autotools-dev (= 20240727.1+nmu1), base-files (= 14.2), base-passwd (= 3.6.8), bash (= 5.3-3), binutils (= 2.46.50.20260617-1), binutils-common (= 2.46.50.20260617-1), binutils-x86-64-linux-gnu (= 2.46.50.20260617-1), bsdextrautils (= 2.42.2-1), build-essential (= 12.12), bzip2 (= 1.0.8-6+b2), coreutils (= 9.10-1), cpp (= 4:15.2.0-5+b1), cpp-15 (= 15.3.0-1), cpp-15-x86-64-linux-gnu (= 15.3.0-1), cpp-x86-64-linux-gnu (= 4:15.2.0-5+b1), dash (= 0.5.12-12), debconf (= 1.5.92), debhelper (= 14.3), debianutils (= 5.23.2), dh-autoreconf (= 22), dh-strip-nondeterminism (= 1.15.1-1), diffutils (= 1:3.12-1), dpkg (= 1.23.7), dpkg-dev (= 1.23.7), dwz (= 0.16-4), file (= 1:5.47-4), findutils (= 4.10.0-4), g++ (= 4:15.2.0-5+b1), g++-15 (= 15.3.0-1), g++-15-x86-64-linux-gnu (= 15.3.0-1), g++-x86-64-linux-gnu (= 4:15.2.0-5+b1), gcc (= 4:15.2.0-5+b1), gcc-15 (= 15.3.0-1), gcc-15-base (= 15.3.0-1), gcc-15-x86-64-linux-gnu (= 15.3.0-1), gcc-16-base (= 16.1.0-2), gcc-x86-64-linux-gnu (= 4:15.2.0-5+b1), gettext (= 1.0-3), gettext-base (= 1.0-3), grep (= 3.12-1), groff-base (= 1.24.1-1), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.4.0-1), libarchive-zip-perl (= 1.68-1), libasan8 (= 16.1.0-2), libatomic1 (= 16.1.0-2), libattr1 (= 1:2.6.0-1), libaudit-common (= 1:4.1.2-1), libaudit1 (= 1:4.1.2-1+b1), libbinutils (= 2.46.50.20260617-1), libblkid1 (= 2.42.2-1), libbz2-1.0 (= 1.0.8-6+b2), libc-bin (= 2.42-17), libc-dev-bin (= 2.42-17), libc-gconv-modules-extra (= 2.42-17), libc6 (= 2.42-17), libc6-dev (= 2.42-17), libcap-ng0 (= 0.9.3-1+b1), libcc1-0 (= 16.1.0-2), libcrypt1 (= 1:4.5.1-1+b1), libctf-nobfd0 (= 2.46.50.20260617-1), libctf0 (= 2.46.50.20260617-1), libdb5.3t64 (= 5.3.28+dfsg2-11+b1), libdebconfclient0 (= 0.283), libdebhelper-perl (= 14.3), libdpkg-perl (= 1.23.7), libelf1t64 (= 0.195-1), libfile-stripnondeterminism-perl (= 1.15.1-1), libgcc-15-dev (= 15.3.0-1), libgcc-s1 (= 16.1.0-2), libgdbm-compat4t64 (= 1.26-1+b2), libgdbm6t64 (= 1.26-1+b2), libgmp10 (= 2:6.3.0+dfsg-5+b2), libgomp1 (= 16.1.0-2), libgprofng0 (= 2.46.50.20260617-1), libhwasan0 (= 16.1.0-2), libisl23 (= 0.27-2), libitm1 (= 16.1.0-2), libjansson4 (= 2.15.1-1), liblsan0 (= 16.1.0-2), liblzma5 (= 5.8.3-1), libmagic-mgc (= 1:5.47-4), libmagic1t64 (= 1:5.47-4), libmd0 (= 1.2.0-2), libmount1 (= 2.42.2-1), libmpc3 (= 1.3.1-3), libmpfr6 (= 4.2.2-3), libpam-modules (= 1.7.0-8), libpam-modules-bin (= 1.7.0-8), libpam-runtime (= 1.7.0-8), libpam0g (= 1.7.0-8), libpcre2-8-0 (= 10.46-1+b2), libperl5.44 (= 5.44.0~rc2-1), libpipeline1 (= 1.5.8-3), libquadmath0 (= 16.1.0-2), libseccomp2 (= 2.6.0-2+b1), libselinux1 (= 3.10-1), libsframe3 (= 2.46.50.20260617-1), libsmartcols1 (= 2.42.2-1), libssl3t64 (= 3.6.3-1), libstdc++-15-dev (= 15.3.0-1), libstdc++6 (= 16.1.0-2), libsystemd0 (= 261.1-2), libtinfo6 (= 6.6+20260608-2), libtool (= 2.5.4-11), libtsan2 (= 16.1.0-2), libubsan1 (= 16.1.0-2), libuchardet0 (= 0.0.8-2+b2), libudev1 (= 261.1-2), libunistring5 (= 1.4.2-1), libuuid1 (= 2.42.2-1), libxml2-16 (= 2.15.3+dfsg-1), libzstd1 (= 1.5.7+dfsg-3+b2), linux-libc-dev (= 7.1.3-1), m4 (= 1.4.21-1), make (= 4.4.1-3), man-db (= 2.13.1-1), mawk (= 1.3.4.20260302-1), ncurses-base (= 6.6+20260608-2), ncurses-bin (= 6.6+20260608-2), openssl-provider-legacy (= 3.6.3-1), patch (= 2.8-2), perl (= 5.44.0~rc2-1), perl-base (= 5.44.0~rc2-1), perl-modules-5.44 (= 5.44.0~rc2-1), po-debconf (= 1.0.22), rpcsvc-proto (= 1.4.4-1), sed (= 4.9-3), sensible-utils (= 0.0.26), sysvinit-utils (= 3.18-1), tar (= 1.35+dfsg-4), util-linux (= 2.42.2-1), xz-utils (= 5.8.3-1), zlib1g (= 1:1.3.dfsg+really1.3.2-3) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LANGUAGE="en_GB:en" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" LD_PRELOAD="libeatmydata.so" SOURCE_DATE_EPOCH="1642340979" +------------------------------------------------------------------------------+ | Package contents Thu, 09 Jul 2026 04:51:00 +0000 | +------------------------------------------------------------------------------+ cct-examples_1.0.3-1_all.deb ---------------------------- new Debian package, version 2.0. size 41893488 bytes: control archive=4072 bytes. 1558 bytes, 30 lines control 14888 bytes, 128 lines md5sums Package: cct-examples Source: cct Version: 1:1.0.3-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 101295 Depends: bioperl, cgview Section: science Priority: optional Homepage: http://stothard.afns.ualberta.ca/downloads/CCT/ Description: example data for testing the package cct The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation. . This package provides the data which can be used as example. These are the same data as used in autopkgtest. drwxr-xr-x root/root 0 2022-01-16 13:49 ./ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/assign_cogs/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/ -rw-r--r-- root/root 202 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_1.gff -rw-r--r-- root/root 1496 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_1b.gff -rw-r--r-- root/root 826 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_2.gff -rw-r--r-- root/root 1401 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/sample_output/sample_2b.gff drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/test_input/ -rw-r--r-- root/root 14693 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/test_input/sample_1.gbk -rw-r--r-- root/root 5869 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/test_input/sample_2.fna drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/cgview_xml_builder/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/ -rw-r--r-- root/root 38162 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/R_denitrificans.cogs -rw-r--r-- root/root 8823242 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/R_denitrificans.gbk -rw-r--r-- root/root 80 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/labels_to_show.txt -rw-r--r-- root/root 13715306 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/test_input/prokka_multicontig.gbk drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/convert_vcf_to_features/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/ -rw-r--r-- root/root 164 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_20 -rw-r--r-- root/root 164 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_20.tab -rw-r--r-- root/root 132 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_21 -rw-r--r-- root/root 132 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_multiple_chromosomes_21.tab -rw-r--r-- root/root 164 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_single_chromosome_20 -rw-r--r-- root/root 164 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/sample_output/output_single_chromosome_20.tab drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/ -rw-r--r-- root/root 1563 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/input_multiple_chromosomes.vcf -rw-r--r-- root/root 1353 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/test_input/input_single_chromosome.vcf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/get_cds/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/ -rw-r--r-- root/root 1525633 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/R_denitrificans.cds.faa -rw-r--r-- root/root 4140742 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/R_denitrificans.cds.fna -rw-r--r-- root/root 2329771 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/prokka_multicontig.cds.faa -rw-r--r-- root/root 6252922 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/sample_output/prokka_multicontig.cds.fna drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/test_input/ -rw-r--r-- root/root 8823242 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/test_input/R_denitrificans.gbk -rw-r--r-- root/root 13715306 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/test_input/prokka_multicontig.gbk drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/get_orfs/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/ -rw-r--r-- root/root 77986 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/R_denitrificans.orfs.faa -rw-r--r-- root/root 228506 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/R_denitrificans.orfs.fna -rw-r--r-- root/root 181045 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/prokka_multicontig.orfs.faa -rw-r--r-- root/root 530920 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/sample_output/prokka_multicontig.orfs.fna drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/test_input/ -rw-r--r-- root/root 8823242 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/test_input/R_denitrificans.gbk -rw-r--r-- root/root 13715306 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/test_input/prokka_multicontig.gbk drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/local_blast_client/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/ -rw-r--r-- root/root 1500 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastn.txt -rw-r--r-- root/root 1380 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastp.txt -rw-r--r-- root/root 2537 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_blastx.txt -rw-r--r-- root/root 1582 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_tblastn.txt -rw-r--r-- root/root 6262 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/sample_output/results_tblastx.txt drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/ -rw-r--r-- root/root 2997 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/test_dna_database.fasta -rw-r--r-- root/root 1365 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/test_input_dna.fasta -rw-r--r-- root/root 406 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/test_input_protein.fasta -rw-r--r-- root/root 1019 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test_input/test_protein_database.fasta drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/ncbi_search/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/sample_output/ -rw-r--r-- root/root 276500 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/sample_output/NC_009933.gbk -rw-r--r-- root/root 8301 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/sample_output/NC_009934.gbk -rw-r--r-- root/root 284801 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/sample_output/combined.gbk drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/ -rw-r--r-- root/root 1696 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output1.fasta -rw-r--r-- root/root 1059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output2.fasta -rw-r--r-- root/root 1059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/output3.fasta -rw-r--r-- root/root 1059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq.fasta -rw-r--r-- root/root 2059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi.fasta -rw-r--r-- root/root 3357 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi_s100_v5.fasta -rw-r--r-- root/root 2059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_multi_v5.fasta -rw-r--r-- root/root 1696 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_s100_v5.fasta -rw-r--r-- root/root 1059 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sample_output/test_seq_v5.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/ -rw-r--r-- root/root 1034 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/test_seq.fasta -rw-r--r-- root/root 2068 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/test_input/test_seq_multi.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/ -rw-r--r-- root/root 383 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/match_end_of_orf.fasta -rw-r--r-- root/root 392 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/match_end_of_orf_rev_comp.fasta -rw-r--r-- root/root 324 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/match_start_of_orf.fasta -rw-r--r-- root/root 333 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/comparison_genomes/match_start_of_orf_rev_comp.fasta -rw-r--r-- root/root 667 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/reference_genome/ -rw-r--r-- root/root 16317 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastn/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/comparison_genomes/ -rw-r--r-- root/root 392 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/comparison_genomes/match_end_of_orf.fasta -rw-r--r-- root/root 324 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/comparison_genomes/match_start_of_orf.fasta -rw-r--r-- root/root 7997 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/reference_genome/ -rw-r--r-- root/root 16317 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastp/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/comparison_genomes/ -rw-r--r-- root/root 392 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/comparison_genomes/match_end_of_orf.fasta -rw-r--r-- root/root 324 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/comparison_genomes/match_start_of_orf.fasta -rw-r--r-- root/root 660 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/reference_genome/ -rw-r--r-- root/root 16317 2022-01-06 22:27 ./usr/share/cct/test_projects/test_blastx/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_orfs/ -rw-r--r-- root/root 632 2022-01-06 22:27 ./usr/share/cct/test_projects/test_orfs/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_orfs/reference_genome/ -rw-r--r-- root/root 3363 2022-01-06 22:27 ./usr/share/cct/test_projects/test_orfs/reference_genome/random.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_plots/ -rw-r--r-- root/root 656 2022-01-06 22:27 ./usr/share/cct/test_projects/test_plots/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_plots/reference_genome/ -rw-r--r-- root/root 5119 2022-01-06 22:27 ./usr/share/cct/test_projects/test_plots/reference_genome/test.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastn/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastn/comparison_genomes/ -rw-r--r-- root/root 383 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_end_of_orf.fasta -rw-r--r-- root/root 392 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_end_of_orf_rev_comp.fasta -rw-r--r-- root/root 324 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_start_of_orf.fasta -rw-r--r-- root/root 333 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastn/comparison_genomes/match_start_of_orf_rev_comp.fasta -rw-r--r-- root/root 7994 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastn/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastn/reference_genome/ -rw-r--r-- root/root 16317 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastn/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastx/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastx/comparison_genomes/ -rw-r--r-- root/root 383 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_end_of_orf.fasta -rw-r--r-- root/root 392 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_end_of_orf_rev_comp.fasta -rw-r--r-- root/root 324 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_start_of_orf.fasta -rw-r--r-- root/root 333 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastx/comparison_genomes/match_start_of_orf_rev_comp.fasta -rw-r--r-- root/root 657 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastx/project_settings.conf drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastx/reference_genome/ -rw-r--r-- root/root 16317 2022-01-06 22:27 ./usr/share/cct/test_projects/test_tblastx/reference_genome/two_copies_of_long_ORF_opposite_directions.fasta drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct-examples/ -rw-r--r-- root/root 926 2022-01-16 13:49 ./usr/share/doc/cct-examples/changelog.Debian.gz -rw-r--r-- root/root 1321 2022-01-16 13:49 ./usr/share/doc/cct-examples/copyright drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/ -rw-r--r-- root/root 4065 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/NC_007717.gbk.gz -rw-r--r-- root/root 3874 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/NC_007718.gbk.gz -rw-r--r-- root/root 4329 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/comparison_genomes/NC_007720.gbk.gz -rw-r--r-- root/root 75 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/labels_to_show.txt -rw-r--r-- root/root 588 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/project_settings_a.conf -rw-r--r-- root/root 592 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/project_settings_b.conf -rw-r--r-- root/root 600 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/project_settings_c.conf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/reference_genome/ -rw-r--r-- root/root 4678 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_1/reference_genome/NC_007719.gbk.gz drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/ -rw-r--r-- root/root 1126402 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/Methanococcus_maripaludis.gbk.gz -rw-r--r-- root/root 3489566 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/Methanosarcina_acetivorans.gbk.gz -rw-r--r-- root/root 1399763 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/comparison_genomes/Thermococcus_kodakaraensis.gbk.gz -rw-r--r-- root/root 588 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/project_settings_a.conf -rw-r--r-- root/root 682 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/project_settings_b.conf -rw-r--r-- root/root 600 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/project_settings_c.conf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/reference_genome/ -rw-r--r-- root/root 1231003 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_2/reference_genome/Methanobacterium_thermoautotrophicum.gbk.gz drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_3/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_3/comparison_genomes/ -rw-r--r-- root/root 3277092 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_3/comparison_genomes/NC_000913.gbk.gz -rw-r--r-- root/root 656 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_3/project_settings_a.conf -rw-r--r-- root/root 654 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_3/project_settings_b.conf -rw-r--r-- root/root 666 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_3/project_settings_c.conf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_3/reference_genome/ -rw-r--r-- root/root 5813038 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_3/reference_genome/NC_004463.gbk.gz drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/analysis/ -rw-r--r-- root/root 307 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/analysis/analysis_1.gff -rw-r--r-- root/root 303 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/analysis/analysis_2.gff drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/comparison_genomes/ -rw-r--r-- root/root 2723 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/comparison_genomes/L09136.gbk.gz -rw-r--r-- root/root 3386 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/comparison_genomes/L09137.gbk.gz drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/features/ -rw-r--r-- root/root 718 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/features/features_1.gff -rw-r--r-- root/root 143 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/features/features_2.gff -rw-r--r-- root/root 667 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/project_settings_a.conf -rw-r--r-- root/root 655 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/project_settings_b.conf -rw-r--r-- root/root 655 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/project_settings_c.conf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/reference_genome/ -rw-r--r-- root/root 2234 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_4/reference_genome/X52329.gbk.gz drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/ -rw-r--r-- root/root 180617 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/Arabidopsis_mito.gbk.gz -rw-r--r-- root/root 3277092 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/E_coli.gbk.gz -rw-r--r-- root/root 14607 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/comparison_genomes/Human_mito.gbk.gz -rw-r--r-- root/root 676 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/project_settings_a.conf -rw-r--r-- root/root 655 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/project_settings_b.conf -rw-r--r-- root/root 655 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/project_settings_c.conf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/reference_genome/ -rw-r--r-- root/root 47129 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_5/reference_genome/NC_001823.gbk.gz drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_6/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_6/comparison_genomes/ -rw-r--r-- root/root 1482 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_6/comparison_genomes/fem.fasta -rw-r--r-- root/root 689 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_6/project_settings_a.conf -rw-r--r-- root/root 690 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_6/project_settings_b.conf -rw-r--r-- root/root 687 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_6/project_settings_c.conf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/sample_projects/sample_project_6/reference_genome/ -rw-r--r-- root/root 7709 2022-01-06 22:27 ./usr/share/doc/cct/examples/sample_projects/sample_project_6/reference_genome/ref.fas.gz lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/examples/test_projects -> ../../../cct/test_projects -rw-r--r-- root/root 419 2022-01-16 13:49 ./usr/share/doc/cct/run-unit-test cct_1.0.3-1_all.deb ------------------- new Debian package, version 2.0. size 36332512 bytes: control archive=3008 bytes. 182 bytes, 5 lines conffiles 1567 bytes, 26 lines control 5454 bytes, 66 lines md5sums Package: cct Version: 1:1.0.3-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 35963 Depends: perl:any, bioperl, cgview, ncbi-blast+-legacy, imagemagick | graphicsmagick, liberror-perl, libtie-ixhash-perl, libwww-perl Section: science Priority: optional Homepage: http://stothard.afns.ualberta.ca/downloads/CCT/ Description: visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences The CGView Comparison Tool (CCT) is a package for visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences of interest to existing genomes or sequence collections. The comparisons are conducted using BLAST, and the BLAST results are presented in the form of graphical maps that can also show sequence features, gene and protein names, COG category assignments, and sequence composition characteristics. CCT can generate maps in a variety of sizes, including 400 Megapixel maps suitable for posters. Comparisons can be conducted within a particular species or genus, or all available genomes can be used. The entire map creation process, from downloading sequences to redrawing zoomed maps, can be completed easily using scripts included with the CCT. User-defined features or analysis results can be included on maps, and maps can be extensively customized. To simplify program setup, a CCT virtual machine that includes all dependencies preinstalled is available. Detailed tutorials illustrating the use of CCT are included with the CCT documentation. drwxr-xr-x root/root 0 2022-01-16 13:49 ./ drwxr-xr-x root/root 0 2022-01-16 13:49 ./etc/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./etc/cct/ -rw-r--r-- root/root 1512 2022-01-16 13:49 ./etc/cct/global_settings.conf -rw-r--r-- root/root 7302 2022-01-06 22:27 ./etc/cct/project_settings.conf -rw-r--r-- root/root 7315 2022-01-06 22:27 ./etc/cct/project_settings_cds_vs_cds.conf -rw-r--r-- root/root 7330 2022-01-06 22:27 ./etc/cct/project_settings_dna_vs_dna.conf -rw-r--r-- root/root 7313 2022-01-06 22:27 ./etc/cct/project_settings_multi.conf drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/bin/ lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/build_blast_atlas -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/build_blast_atlas_all_vs_all -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/build_cog_db -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/cgview_comparison_tool -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/check_env -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/convert_vcf_to_features -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/create_zoomed_maps -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/fetch_all_refseq_bacterial_genomes -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/fetch_all_refseq_chloroplast_genomes -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/fetch_all_refseq_mitochondrial_genomes -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/fetch_genome_by_accession -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/fetch_refseq_bacterial_genomes_by_name -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/ncbi_search -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/process_sample_projects -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/process_test_projects -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/redraw_maps -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/remove_long_seqs -> ../share/cct/scripts/generic lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/bin/remove_short_seqs -> ../share/cct/scripts/generic drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/ lrwxrwxrwx root/root 0 2022-01-16 13:49 ./usr/share/cct/conf -> /etc/cct drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/assign_cogs/ -rw-r--r-- root/root 4000 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/README.md -rwxr-xr-x root/root 17690 2022-01-06 22:27 ./usr/share/cct/lib/scripts/assign_cogs/assign_cogs.pl drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/assign_cogs/db/ -rw-r--r-- root/root 35548721 2022-01-16 13:49 ./usr/share/cct/lib/scripts/assign_cogs/db/myva.gz -rw-r--r-- root/root 693835 2022-01-16 13:49 ./usr/share/cct/lib/scripts/assign_cogs/db/whog.gz -rwxr-xr-x root/root 1561 2022-01-16 13:49 ./usr/share/cct/lib/scripts/assign_cogs/test.sh drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/cgview_xml_builder/ -rw-r--r-- root/root 12925 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/README.md -rwxr-xr-x root/root 196570 2022-01-06 22:27 ./usr/share/cct/lib/scripts/cgview_xml_builder/cgview_xml_builder.pl -rwxr-xr-x root/root 3655 2022-01-16 13:49 ./usr/share/cct/lib/scripts/cgview_xml_builder/test.sh drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/convert_vcf_to_features/ -rw-r--r-- root/root 1373 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/README.md -rwxr-xr-x root/root 3579 2022-01-16 13:49 ./usr/share/cct/lib/scripts/convert_vcf_to_features/convert_vcf_to_features.pl -rwxr-xr-x root/root 1118 2022-01-06 22:27 ./usr/share/cct/lib/scripts/convert_vcf_to_features/test.sh drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/get_cds/ -rw-r--r-- root/root 1397 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/README.md -rwxr-xr-x root/root 7150 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/get_cds.pl -rwxr-xr-x root/root 1021 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_cds/test.sh drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/get_orfs/ -rw-r--r-- root/root 2131 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/README.md -rwxr-xr-x root/root 6915 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/get_orfs.pl -rwxr-xr-x root/root 1061 2022-01-06 22:27 ./usr/share/cct/lib/scripts/get_orfs/test.sh drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/local_blast_client/ -rw-r--r-- root/root 2684 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/README.md -rwxr-xr-x root/root 16601 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/local_blast_client.pl -rwxr-xr-x root/root 2200 2022-01-06 22:27 ./usr/share/cct/lib/scripts/local_blast_client/test.sh drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/ncbi_search/ -rw-r--r-- root/root 7116 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/README.md -rwxr-xr-x root/root 7673 2022-01-16 13:49 ./usr/share/cct/lib/scripts/ncbi_search/ncbi_search.pl -rwxr-xr-x root/root 864 2022-01-06 22:27 ./usr/share/cct/lib/scripts/ncbi_search/test.sh drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/ -rw-r--r-- root/root 1611 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/README.md -rwxr-xr-x root/root 3898 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/sequence_to_multi_fasta.pl -rwxr-xr-x root/root 1279 2022-01-06 22:27 ./usr/share/cct/lib/scripts/sequence_to_multi_fasta/test.sh drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/cct/scripts/ -rwxr-xr-x root/root 9530 2022-01-06 22:27 ./usr/share/cct/scripts/build_blast_atlas.sh -rwxr-xr-x root/root 10420 2022-01-06 22:27 ./usr/share/cct/scripts/build_blast_atlas_all_vs_all.sh -rwxr-xr-x root/root 1276 2022-01-16 13:49 ./usr/share/cct/scripts/build_cog_db.sh -rwxr-xr-x root/root 75134 2022-01-16 13:49 ./usr/share/cct/scripts/cgview_comparison_tool.pl -rwxr-xr-x root/root 2219 2022-01-06 22:27 ./usr/share/cct/scripts/check_env.sh -rwxr-xr-x root/root 3579 2022-01-16 13:49 ./usr/share/cct/scripts/convert_vcf_to_features.pl -rwxr-xr-x root/root 3050 2022-01-16 13:49 ./usr/share/cct/scripts/create_zoomed_maps.sh -rwxr-xr-x root/root 2440 2022-01-06 22:27 ./usr/share/cct/scripts/fetch_all_refseq_bacterial_genomes.sh -rwxr-xr-x root/root 1732 2022-01-06 22:27 ./usr/share/cct/scripts/fetch_all_refseq_chloroplast_genomes.sh -rwxr-xr-x root/root 1620 2022-01-06 22:27 ./usr/share/cct/scripts/fetch_all_refseq_mitochondrial_genomes.sh -rwxr-xr-x root/root 2016 2022-01-06 22:27 ./usr/share/cct/scripts/fetch_genome_by_accession.sh -rwxr-xr-x root/root 2747 2022-01-06 22:27 ./usr/share/cct/scripts/fetch_refseq_bacterial_genomes_by_name.sh -rwxr-xr-x root/root 512 2022-01-16 13:49 ./usr/share/cct/scripts/generic -rwxr-xr-x root/root 7673 2022-01-16 13:49 ./usr/share/cct/scripts/ncbi_search.pl -rwxr-xr-x root/root 1369 2022-01-06 22:27 ./usr/share/cct/scripts/process_sample_projects.sh -rwxr-xr-x root/root 1316 2022-01-16 13:49 ./usr/share/cct/scripts/process_test_projects.sh -rwxr-xr-x root/root 2407 2022-01-16 13:49 ./usr/share/cct/scripts/redraw_maps.sh -rwxr-xr-x root/root 2226 2022-01-06 22:27 ./usr/share/cct/scripts/remove_long_seqs.sh -rwxr-xr-x root/root 2474 2022-01-06 22:27 ./usr/share/cct/scripts/remove_short_seqs.sh drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/doc/cct/ -rw-r--r-- root/root 300 2022-01-16 13:49 ./usr/share/doc/cct/README.Debian -rw-r--r-- root/root 2202 2022-01-06 22:27 ./usr/share/doc/cct/README.md.gz -rw-r--r-- root/root 318 2022-01-16 13:49 ./usr/share/doc/cct/README.test -rw-r--r-- root/root 923 2022-01-16 13:49 ./usr/share/doc/cct/changelog.Debian.gz -rw-r--r-- root/root 1321 2022-01-16 13:49 ./usr/share/doc/cct/copyright drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/man/ drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/man/man1/ -rw-r--r-- root/root 1511 2022-01-16 13:49 ./usr/share/man/man1/build_blast_atlas.1.gz -rw-r--r-- root/root 1554 2022-01-16 13:49 ./usr/share/man/man1/build_blast_atlas_all_vs_all.1.gz -rw-r--r-- root/root 1546 2022-01-16 13:49 ./usr/share/man/man1/cgview_comparison_tool.1.gz -rw-r--r-- root/root 606 2022-01-16 13:49 ./usr/share/man/man1/convert_vcf_to_features.1.gz -rw-r--r-- root/root 660 2022-01-16 13:49 ./usr/share/man/man1/create_zoomed_maps.1.gz -rw-r--r-- root/root 642 2022-01-16 13:49 ./usr/share/man/man1/fetch_all_refseq_bacterial_genomes.1.gz -rw-r--r-- root/root 530 2022-01-16 13:49 ./usr/share/man/man1/fetch_all_refseq_chloroplast_genomes.1.gz -rw-r--r-- root/root 532 2022-01-16 13:49 ./usr/share/man/man1/fetch_all_refseq_mitochondrial_genomes.1.gz -rw-r--r-- root/root 553 2022-01-16 13:49 ./usr/share/man/man1/fetch_genome_by_accession.1.gz -rw-r--r-- root/root 701 2022-01-16 13:49 ./usr/share/man/man1/fetch_refseq_bacterial_genomes_by_name.1.gz -rw-r--r-- root/root 959 2022-01-16 13:49 ./usr/share/man/man1/ncbi_search.1.gz -rw-r--r-- root/root 610 2022-01-16 13:49 ./usr/share/man/man1/redraw_maps.1.gz -rw-r--r-- root/root 566 2022-01-16 13:49 ./usr/share/man/man1/remove_long_seqs.1.gz -rw-r--r-- root/root 623 2022-01-16 13:49 ./usr/share/man/man1/remove_short_seqs.1.gz drwxr-xr-x root/root 0 2022-01-16 13:49 ./usr/share/perl5/ drwxr-xr-x root/root 0 2022-01-06 22:27 ./usr/share/perl5/Util/ -rw-r--r-- root/root 5229 2022-01-06 22:27 ./usr/share/perl5/Util/Configurator.pm -rw-r--r-- root/root 6677 2022-01-06 22:27 ./usr/share/perl5/Util/LogManager.pm +------------------------------------------------------------------------------+ | Post Build Thu, 09 Jul 2026 04:51:02 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Thu, 09 Jul 2026 04:51:02 +0000 | +------------------------------------------------------------------------------+ Purging /build/cct-04sq6m Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Thu, 09 Jul 2026 04:51:03 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 488980 Build-Time: 132 Distribution: perl-5.44-throwaway Host Architecture: amd64 Install-Time: 6 Job: /srv/debomatic/incoming/cct_1.0.3-1.dsc Machine Architecture: amd64 Package: cct Package-Time: 147 Source-Version: 1:1.0.3-1 Space: 488980 Status: successful Version: 1:1.0.3-1 -------------------------------------------------------------------------------- Finished at 2026-07-09T04:50:59Z Build needed 00:02:27, 488980k disk space