sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk +==============================================================================+ | trim-galore 0.6.10-1 (amd64) Wed, 05 Jun 2024 11:49:28 +0000 | +==============================================================================+ Package: trim-galore Version: 0.6.10-1 Source Version: 0.6.10-1 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-c405ba7d-2f4d-44fd-9c15-51c508bcc851' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup trim-galore_0.6.10-1 perl-5.40-throwaway amd64 --------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup trim-galore_0.6.10-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/trim-galore-h0T2MF/resolver-M9U6kS' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B] Get:2 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB] Get:3 http://localhost:3142/debian unstable InRelease [198 kB] Get:4 http://localhost:3142/debian sid InRelease [198 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-05-0804.11-F-2024-06-03-0205.12.pdiff [122 kB] Get:6 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-05-0804.11-F-2024-06-03-0205.12.pdiff [122 kB] Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-05-0804.11-F-2024-06-03-0205.12.pdiff [83.8 kB] Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-05-0804.11-F-2024-06-03-0205.12.pdiff [83.8 kB] Fetched 730 kB in 7s (102 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils libblkid1 libmount1 libsmartcols1 libssl3t64 libuuid1 login passwd util-linux 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5660 kB of archives. After this operation, 53.2 kB disk space will be freed. Get:1 http://localhost:3142/debian unstable/main amd64 bsdutils amd64 1:2.40.1-8 [104 kB] Get:2 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.13+dfsg1-5 [590 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libsmartcols1 amd64 2.40.1-8 [137 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libuuid1 amd64 2.40.1-8 [34.7 kB] Get:5 http://localhost:3142/debian unstable/main amd64 libblkid1 amd64 2.40.1-8 [166 kB] Get:6 http://localhost:3142/debian unstable/main amd64 libmount1 amd64 2.40.1-8 [197 kB] Get:7 http://localhost:3142/debian unstable/main amd64 util-linux amd64 2.40.1-8 [1210 kB] Get:8 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.13+dfsg1-5 [974 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libssl3t64 amd64 3.2.2-1 [2246 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5660 kB in 0s (141 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/trim-galore_0.6.10-1.dsc exists in /srv/debomatic/incoming; copying to chroot I: NOTICE: Log filtering will replace 'build/trim-galore-h0T2MF/trim-galore-0.6.10' with '<>' I: NOTICE: Log filtering will replace 'build/trim-galore-h0T2MF' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 13), 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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [617 B] Get:5 copy:/<>/apt_archive ./ Packages [649 B] Fetched 1875 B in 0s (0 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 additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx 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 fakeroot file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 32 newly installed, 0 to remove and 0 not upgraded. Need to get 19.1 MB of archives. After this operation, 73.9 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [880 B] Get:2 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:5 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB] Get:6 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB] Get:7 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB] Get:8 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB] Get:9 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-8 [96.0 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB] Get:11 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB] Get:12 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:13 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB] Get:14 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:15 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:16 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB] Get:18 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB] Get:19 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:22 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:23 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB] Get:24 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:25 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB] Get:27 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB] Get:28 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:29 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:30 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB] Get:32 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.1 MB in 0s (140 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 21765 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.45-3_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.45-3_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.45-3) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.45-3_amd64.deb ... Unpacking file (1:5.45-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.21-14+b1_amd64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../05-libuchardet0_0.0.8-1+b1_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.8-1+b1) ... 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Unpacking libxml2:amd64 (2.12.7+dfsg-3) ... Selecting previously unselected package gettext. Preparing to unpack .../25-gettext_0.21-14+b1_amd64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../26-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 .../27-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../28-debhelper_13.15.3_all.deb ... Unpacking debhelper (13.15.3) ... Selecting previously unselected package libfakeroot:amd64. Preparing to unpack .../29-libfakeroot_1.34-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.34-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../30-fakeroot_1.34-1_amd64.deb ... Unpacking fakeroot (1.34-1) ... Selecting previously unselected package sbuild-build-depends-main-dummy. Preparing to unpack .../31-sbuild-build-depends-main-dummy_0.invalid.0_amd64.deb ... Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ... Setting up libpipeline1:amd64 (1.5.7-2) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up bsdextrautils (2.40.1-8) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.15.3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up file (1:5.45-3) ... Setting up libfakeroot:amd64 (1.34-1) ... Setting up libelf1t64:amd64 (0.191-1+b1) ... Setting up fakeroot (1.34-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:amd64 (0.0.8-1+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up gettext (0.21-14+b1) ... Setting up libtool (2.4.7-7) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-4) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.15.3) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.38-12) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64) Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1 Package versions: adduser_3.137 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40.1-8 bsdutils_1:2.40.1-8 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libasan8_14.1.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libblkid1_2.40.1-8 libbz2-1.0_1.0.8-5.1 libc-bin_2.38-12 libc-dev-bin_2.38-12 libc-l10n_2.38-12 libc6_2.38-12 libc6-dev_2.38-12 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14.1.0-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-4 libctf0_2.42-4 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.15.3 libdpkg-perl_1.22.6 libeatmydata1_131-2 libelf1t64_0.191-1+b1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.2.0-25 libgcc-s1_14.1.0-1 libgcrypt20_1.10.3-3 libgdbm-compat4t64_1.23-5.1+b1 libgdbm6t64_1.23-5.1+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-4 libgomp1_14.1.0-1 libgpg-error0_1.49-2 libgprofng0_2.42-4 libhogweed6t64_3.9.1-2.2 libhwasan0_14.1.0-1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.1.0-1 libjansson4_2.14-2+b2 libksba8_1.6.6-1 libldap-2.5-0_2.5.17+dfsg-1+b1 liblsan0_14.1.0-1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.1-8 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.9.1-2.2 libnpth0t64_1.6-3.1 libp11-kit0_0.25.3-5 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0~rc1-1 libpipeline1_1.5.7-2 libquadmath0_14.1.0-1 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1 libselinux1_3.5-2+b2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b3 libsepol2_3.5-2+b1 libsframe1_2.42-4 libsmartcols1_2.40.1-8 libsqlite3-0_3.46.0-1 libssl3t64_3.2.2-1 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 libsystemd0_256~rc3-7 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.1.0-1 libubsan1_14.1.0-1 libuchardet0_0.0.8-1+b1 libudev1_256~rc3-7 libunistring5_1.2-1 libuuid1_2.40.1-8 libxml2_2.12.7+dfsg-3 libxxhash0_0.8.2-2+b1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.12-1 locales-all_2.38-12 login_1:4.13+dfsg1-5 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.13+dfsg1-5 patch_2.7.6-7 perl_5.40.0~rc1-1 perl-base_5.40.0~rc1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0~rc1-1 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.09-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.1-8 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: trim-galore Binary: trim-galore Architecture: all Version: 0.6.10-1 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller Homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/trim-galore Vcs-Git: https://salsa.debian.org/med-team/trim-galore.git Testsuite: autopkgtest Testsuite-Triggers: build-essential Build-Depends: debhelper-compat (= 13) Package-List: trim-galore deb science optional arch=all Checksums-Sha1: dd1320b1efb03f9ee57bb1ee021746a686e83ec7 26831358 trim-galore_0.6.10.orig.tar.gz f873bbd10ee072e43990e6ad12c2f597614864b4 10796 trim-galore_0.6.10-1.debian.tar.xz Checksums-Sha256: 3a4e414fc658d6eb4356f1572351204e8475a9d7dc79f6798270b57d35bda017 26831358 trim-galore_0.6.10.orig.tar.gz 3977f48b27fe4ec7f21ae363eb22fa618d476d5b78d0826daeb94c20d2741c29 10796 trim-galore_0.6.10-1.debian.tar.xz Files: ce8ea65db052838656fd3d760c17d9f9 26831358 trim-galore_0.6.10.orig.tar.gz c485f4f2566efcfb88ba74802ddc9452 10796 trim-galore_0.6.10-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPgEYARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFp7Q//T5CkpDRQmXldC9TnTUPKc+9DsZlKog0p zctsO1n3xQRxHD7BP2nnPpJUdurxrbE/KkugEoRAYeHOpQps3UdBxTJkfVOtRUrt qg8N6okXCm4KIU/HthcuUi2xQFbUQ1rcRAwPsgyI4AWuSkFvvtXPkn83aeRvtaHQ 4y8XbpqOQ8LK9kBIchY5kA0zclNFh9elYMwIga15Z/syw1RgOdoSOIvInqtTuw4k ZfFonCS9vJeEoTWyuYZA3hXb7jAeYgxiXslcNTgwtXinBGJ/8/odEVslh//pzU9C 8aMW1gyEVoWdaW31MAPnWHhjoi6jsmpgk5ARl/GiUKE5BlxuAgDcqDRM1B/EWdRp BmoqNp19sMHBG2y5P9VUK5Vp6XrHvmukmkzUGIgA4EHsfs/wjUzfAgZvmefJoGhK ZyD1znWZJaIhQuljLGFZq9yYNb5LBcNQyofB/VGrkZIKuO1gDtFNhDayqOaT5PyF wZSyeL9rC8GgrYt6XhOxAoCoUqdCa/eprQihYaVhLiRnNjcTWmpXCLaYEkeSkPMy 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trim-galore_0.6.10-1 perl-5.40-throwaway amd64 --------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network trim-galore_0.6.10-1 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 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=/<> SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-c405ba7d-2f4d-44fd-9c15-51c508bcc851 SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz dpkg-buildpackage: info: source package trim-galore dpkg-buildpackage: info: source version 0.6.10-1 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 rm -f debian/debhelper-build-stamp rm -rf debian/.debhelper/ rm -f -- debian/trim-galore.substvars debian/files rm -fr -- debian/trim-galore/ debian/tmp/ find . \( \( \ \( -path .\*/.git -o -path .\*/.svn -o -path .\*/.bzr -o -path .\*/.hg -o -path .\*/CVS -o -path .\*/.pc -o -path .\*/_darcs \) -prune -o -type f -a \ \( -name '#*#' -o -name '.*~' -o -name '*~' -o -name DEADJOE \ -o -name '*.orig' -o -name '*.rej' -o -name '*.bak' \ -o -name '.*.orig' -o -name .*.rej -o -name '.SUMS' \ -o -name TAGS -o \( -path '*/.deps/*' -a -name '*.P' \) \ \) -exec rm -f {} + \) -o \ \( -type d -a \( -name autom4te.cache -o -name __pycache__ \) -prune -exec rm -rf {} + \) \) dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building trim-galore using existing ./trim-galore_0.6.10.orig.tar.gz dpkg-source: info: building trim-galore in trim-galore_0.6.10-1.debian.tar.xz dpkg-source: info: building trim-galore in trim-galore_0.6.10-1.dsc debian/rules binary dh binary dh_update_autotools_config dh_autoreconf create-stamp debian/debhelper-build-stamp dh_prep rm -f -- debian/trim-galore.substvars rm -fr -- debian/.debhelper/generated/trim-galore/ debian/trim-galore/ debian/tmp/ dh_auto_install --destdir=debian/trim-galore/ install -m0755 -d /<>/debian/trim-galore dh_install install -m0755 -d debian/trim-galore/usr/bin cp --reflink=auto -a ./trim_galore debian/trim-galore/usr/bin/ dh_installdocs install -m0755 -d debian/trim-galore/usr/share/doc/trim-galore install -p -m0644 debian/copyright debian/trim-galore/usr/share/doc/trim-galore/copyright dh_installchangelogs install -m0755 -d debian/trim-galore/usr/share/doc/trim-galore install -p -m0644 debian/.debhelper/generated/trim-galore/dh_installchangelogs.dch.trimmed debian/trim-galore/usr/share/doc/trim-galore/changelog.Debian install -p -m0644 ./CHANGELOG.md debian/trim-galore/usr/share/doc/trim-galore/changelog debian/rules override_dh_installexamples make[1]: Entering directory '/<>' dh_installexamples install -m0755 -d debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/4_seqs_with_Ns.fastq.gz debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/clock_10K_R1.fastq.gz debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/clock_10K_R2.fastq.gz debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/colorspace_file.fastq debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/empty_file.fastq debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/illumina_100K.fastq.gz debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/illumina_100K.fastq.gz_trimming_report.txt debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/illumina_10K.fastq.gz debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/illumina_10K.fastq.gz_trimming_report.txt debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/illumina_10K_trimmed.fq.gz debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/nextera_100K.fastq.gz debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/nextera_100K.fastq.gz_trimming_report.txt debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/smallRNA_100K.fastq.gz debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/smallRNA_100K.fastq.gz_trimming_report.txt debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/smallRNA_100K_R1.fastq.gz_trimming_report.txt debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/smallRNA_100K_R2.fastq.gz debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/smallRNA_100K_R2.fastq.gz_trimming_report.txt debian/trim-galore/usr/share/doc/trim-galore/examples cp --reflink=auto -a ./test_files/truncated.fq.gz debian/trim-galore/usr/share/doc/trim-galore/examples rm -rf debian/trim-galore/usr/share/doc/trim-galore/examples/truncated.fq.gz \ debian/trim-galore/usr/share/doc/trim-galore/examples/smallRNA_100K_R2.fastq.gz \ debian/trim-galore/usr/share/doc/trim-galore/examples/*.fastq \ debian/trim-galore/usr/share/doc/trim-galore/examples/*.txt make[1]: Leaving directory '/<>' dh_installman install -m0755 -d debian/trim-galore/usr/share/man/man1/ install -p -m0644 ./debian/trim_galore.1 debian/trim-galore/usr/share/man/man1/trim_galore.1 man-recode --to-code UTF-8 --suffix .dh-new debian/trim-galore/usr/share/man/man1/trim_galore.1 mv debian/trim-galore/usr/share/man/man1/trim_galore.1.dh-new debian/trim-galore/usr/share/man/man1/trim_galore.1 chmod 0644 -- debian/trim-galore/usr/share/man/man1/trim_galore.1 dh_lintian install -m0755 -d debian/trim-galore/usr/share/lintian/overrides install -p -m0644 debian/lintian-overrides debian/trim-galore/usr/share/lintian/overrides/trim-galore dh_perl mv debian/trim-galore.substvars.new debian/trim-galore.substvars dh_link dh_strip_nondeterminism Using 1675627531 as canonical time Normalizing debian/trim-galore/usr/share/doc/trim-galore/examples/4_seqs_with_Ns.fastq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/trim-galore/usr/share/doc/trim-galore/examples/clock_10K_R2.fastq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/trim-galore/usr/share/doc/trim-galore/examples/smallRNA_100K.fastq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/trim-galore/usr/share/doc/trim-galore/examples/nextera_100K.fastq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/trim-galore/usr/share/doc/trim-galore/examples/illumina_10K_trimmed.fq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/trim-galore/usr/share/doc/trim-galore/examples/clock_10K_R1.fastq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/trim-galore/usr/share/doc/trim-galore/examples/illumina_100K.fastq.gz using File::StripNondeterminism::handlers::gzip Normalizing debian/trim-galore/usr/share/doc/trim-galore/examples/illumina_10K.fastq.gz using File::StripNondeterminism::handlers::gzip dh_compress cd debian/trim-galore chmod a-x usr/share/doc/trim-galore/changelog usr/share/doc/trim-galore/changelog.Debian usr/share/man/man1/trim_galore.1 gzip -9nf usr/share/doc/trim-galore/changelog usr/share/doc/trim-galore/changelog.Debian usr/share/man/man1/trim_galore.1 cd '/<>' dh_fixperms find debian/trim-galore ! -type l -a -true -a -true -print0 2>/dev/null | xargs -0r chmod go=rX,u+rw,a-s find debian/trim-galore/usr/share/doc -type f -a -true -a ! -regex 'debian/trim-galore/usr/share/doc/[^/]*/examples/.*' -print0 2>/dev/null | xargs -0r chmod 0644 find debian/trim-galore/usr/share/doc -type d -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0755 find debian/trim-galore/usr/share/man debian/trim-galore/usr/share/lintian/overrides -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/trim-galore -type f \( -name '*.so.*' -o -name '*.so' -o -name '*.la' -o -name '*.a' -o -name '*.js' -o -name '*.css' -o -name '*.scss' -o -name '*.sass' -o -name '*.jpeg' -o -name '*.jpg' -o -name '*.png' -o -name '*.gif' -o -name '*.cmxs' -o -name '*.node' \) -a -true -a -true -print0 2>/dev/null | xargs -0r chmod 0644 find debian/trim-galore/usr/bin -type f -a -true -a -true -print0 2>/dev/null | xargs -0r chmod a+x dh_missing dh_installdeb install -m0755 -d debian/trim-galore/DEBIAN dh_gencontrol install -m0755 -d debian/trim-galore/DEBIAN echo misc:Depends= >> debian/trim-galore.substvars echo misc:Pre-Depends= >> debian/trim-galore.substvars dpkg-gencontrol -ptrim-galore -ldebian/changelog -Tdebian/trim-galore.substvars -cdebian/control -Pdebian/trim-galore chmod 0644 -- debian/trim-galore/DEBIAN/control dh_md5sums install -m0755 -d debian/trim-galore/DEBIAN cd debian/trim-galore >/dev/null && xargs -r0 md5sum | perl -pe 'if (s@^\\@@) { s/\\\\/\\/g; }' > DEBIAN/md5sums chmod 0644 -- debian/trim-galore/DEBIAN/md5sums dh_builddeb dpkg-deb --root-owner-group --build debian/trim-galore .. dpkg-deb: building package 'trim-galore' in '../trim-galore_0.6.10-1_all.deb'. dpkg-genbuildinfo -O../trim-galore_0.6.10-1_amd64.buildinfo dpkg-genchanges -O../trim-galore_0.6.10-1_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 2024-06-05T11:49:55Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ trim-galore_0.6.10-1_amd64.changes: ----------------------------------- Format: 1.8 Date: Sun, 05 Feb 2023 21:05:31 +0100 Source: trim-galore Binary: trim-galore Architecture: source all Version: 0.6.10-1 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: trim-galore - automate quality and adapter trimming for DNA sequencing Changes: trim-galore (0.6.10-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.6.2 (routine-update) Checksums-Sha1: 9dbb580fd618000b08b69ef8750a0abceb7e269e 1169 trim-galore_0.6.10-1.dsc 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optional trim-galore_0.6.10.orig.tar.gz c485f4f2566efcfb88ba74802ddc9452 10796 science optional trim-galore_0.6.10-1.debian.tar.xz e012e0e275f1f0018bdc6a632f7a5ba4 17819680 science optional trim-galore_0.6.10-1_all.deb d76167262f3f26759e326f57cdec631d 4919 science optional trim-galore_0.6.10-1_amd64.buildinfo +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: trim-galore Binary: trim-galore Architecture: all source Version: 0.6.10-1 Checksums-Md5: 28024247ddb9f84e6b7c20db00a2e89a 1169 trim-galore_0.6.10-1.dsc e012e0e275f1f0018bdc6a632f7a5ba4 17819680 trim-galore_0.6.10-1_all.deb Checksums-Sha1: 9dbb580fd618000b08b69ef8750a0abceb7e269e 1169 trim-galore_0.6.10-1.dsc 0c09f9962749566fea5a997929249e63e4d77eaf 17819680 trim-galore_0.6.10-1_all.deb Checksums-Sha256: 986afe2c30c7ae1069f48c1216772ce580ad41ed1b267458b869306f9c27865a 1169 trim-galore_0.6.10-1.dsc 76b6a5b9ceed3089b667a2636393ad49998e85b01bf10e63ca37f53105278de3 17819680 trim-galore_0.6.10-1_all.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 05 Jun 2024 11:49:54 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13.2), base-passwd (= 3.6.3), bash (= 5.2.21-2+b1), binutils (= 2.42-4), binutils-common (= 2.42-4), binutils-x86-64-linux-gnu (= 2.42-4), bsdextrautils (= 2.40.1-8), bsdutils (= 1:2.40.1-8), build-essential (= 12.10), bzip2 (= 1.0.8-5.1), coreutils (= 9.4-3.1), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-25), cpp-13-x86-64-linux-gnu (= 13.2.0-25), cpp-x86-64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-8), debconf (= 1.5.86), debhelper (= 13.15.3), debianutils (= 5.17), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.0-1), diffutils (= 1:3.10-1), dpkg (= 1.22.6), dpkg-dev (= 1.22.6), dwz (= 0.15-1+b1), file (= 1:5.45-3), findutils (= 4.9.0-6), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-25), g++-13-x86-64-linux-gnu (= 13.2.0-25), g++-x86-64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-25), gcc-13-base (= 13.2.0-25), gcc-13-x86-64-linux-gnu (= 13.2.0-25), gcc-14-base (= 14.1.0-1), gcc-x86-64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+b1), grep (= 3.11-4), groff-base (= 1.23.0-4), gzip (= 1.12-1.1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.1.0-1), libatomic1 (= 14.1.0-1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-4), libblkid1 (= 2.40.1-8), libbz2-1.0 (= 1.0.8-5.1), libc-bin (= 2.38-12), libc-dev-bin (= 2.38-12), libc6 (= 2.38-12), libc6-dev (= 2.38-12), libcap-ng0 (= 0.8.5-1), libcap2 (= 1:2.66-5), libcc1-0 (= 14.1.0-1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-4), libctf0 (= 2.42-4), libdb5.3t64 (= 5.3.28+dfsg2-7), libdebconfclient0 (= 0.272), libdebhelper-perl (= 13.15.3), libdpkg-perl (= 1.22.6), libelf1t64 (= 0.191-1+b1), libfile-stripnondeterminism-perl (= 1.14.0-1), libgcc-13-dev (= 13.2.0-25), libgcc-s1 (= 14.1.0-1), libgdbm-compat4t64 (= 1.23-5.1+b1), libgdbm6t64 (= 1.23-5.1+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14.1.0-1), libgprofng0 (= 2.42-4), libhwasan0 (= 14.1.0-1), libicu72 (= 72.1-4+b1), libisl23 (= 0.26-3+b2), libitm1 (= 14.1.0-1), libjansson4 (= 2.14-2+b2), liblsan0 (= 14.1.0-1), liblzma5 (= 5.6.1+really5.4.5-1), libmagic-mgc (= 1:5.45-3), libmagic1t64 (= 1:5.45-3), libmd0 (= 1.1.0-2), libmount1 (= 2.40.1-8), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libpam-modules (= 1.5.3-7), libpam-modules-bin (= 1.5.3-7), libpam-runtime (= 1.5.3-7), libpam0g (= 1.5.3-7), libpcre2-8-0 (= 10.42-4+b1), libperl5.40 (= 5.40.0~rc1-1), libpipeline1 (= 1.5.7-2), libquadmath0 (= 14.1.0-1), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-2+b2), libsframe1 (= 2.42-4), libsmartcols1 (= 2.40.1-8), libssl3t64 (= 3.2.2-1), libstdc++-13-dev (= 13.2.0-25), libstdc++6 (= 14.1.0-1), libsystemd0 (= 256~rc3-7), libtinfo6 (= 6.5-2), libtool (= 2.4.7-7), libtsan2 (= 14.1.0-1), libubsan1 (= 14.1.0-1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 256~rc3-7), libunistring5 (= 1.2-1), libuuid1 (= 2.40.1-8), libxml2 (= 2.12.7+dfsg-3), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.8.12-1), login (= 1:4.13+dfsg1-5), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.1-1), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.5-2), ncurses-bin (= 6.5-2), patch (= 2.7.6-7), perl (= 5.40.0~rc1-1), perl-base (= 5.40.0~rc1-1), perl-modules-5.40 (= 5.40.0~rc1-1), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.09-1), tar (= 1.35+dfsg-3), usr-is-merged (= 39), util-linux (= 2.40.1-8), xz-utils (= 5.6.1+really5.4.5-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1675627531" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ trim-galore_0.6.10-1_all.deb ---------------------------- new Debian package, version 2.0. size 17819680 bytes: control archive=1816 bytes. 2271 bytes, 39 lines control 1158 bytes, 14 lines md5sums Package: trim-galore Version: 0.6.10-1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 17528 Depends: perl:any, cutadapt Recommends: fastqc Section: science Priority: optional Homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Description: automate quality and adapter trimming for DNA sequencing Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are: * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too * For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation * For any kind of FastQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter- and quality trimming * The Phred quality of basecalls and the stringency for adapter removal can be specified individually * Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality * Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1 * Trim Galore! accepts and produces standard or gzip compressed FastQ files * FastQC can optionally be run on the resulting output files once trimming has completed drwxr-xr-x root/root 0 2023-02-05 20:05 ./ drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/ drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/bin/ -rwxr-xr-x root/root 142076 2023-02-02 11:25 ./usr/bin/trim_galore drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/share/ drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/share/doc/ drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/share/doc/trim-galore/ -rw-r--r-- root/root 830 2023-02-05 20:05 ./usr/share/doc/trim-galore/changelog.Debian.gz -rw-r--r-- root/root 8401 2023-02-02 11:25 ./usr/share/doc/trim-galore/changelog.gz -rw-r--r-- root/root 1121 2023-02-05 20:05 ./usr/share/doc/trim-galore/copyright drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/share/doc/trim-galore/examples/ -rw-r--r-- root/root 298 2023-02-05 20:05 ./usr/share/doc/trim-galore/examples/4_seqs_with_Ns.fastq.gz -rw-r--r-- root/root 404819 2023-02-05 20:05 ./usr/share/doc/trim-galore/examples/clock_10K_R1.fastq.gz -rw-r--r-- root/root 398786 2023-02-05 20:05 ./usr/share/doc/trim-galore/examples/clock_10K_R2.fastq.gz -rw-r--r-- root/root 9612997 2023-02-05 20:05 ./usr/share/doc/trim-galore/examples/illumina_100K.fastq.gz -rw-r--r-- root/root 983203 2023-02-05 20:05 ./usr/share/doc/trim-galore/examples/illumina_10K.fastq.gz -rw-r--r-- root/root 864765 2023-02-05 20:05 ./usr/share/doc/trim-galore/examples/illumina_10K_trimmed.fq.gz -rw-r--r-- root/root 3411557 2023-02-05 20:05 ./usr/share/doc/trim-galore/examples/nextera_100K.fastq.gz -rw-r--r-- root/root 2091317 2023-02-05 20:05 ./usr/share/doc/trim-galore/examples/smallRNA_100K.fastq.gz drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/share/lintian/ drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/share/lintian/overrides/ -rw-r--r-- root/root 65 2023-02-05 20:05 ./usr/share/lintian/overrides/trim-galore drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/share/man/ drwxr-xr-x root/root 0 2023-02-05 20:05 ./usr/share/man/man1/ -rw-r--r-- root/root 7477 2023-02-05 20:05 ./usr/share/man/man1/trim_galore.1.gz +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 88160 Build-Time: 10 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 5 Job: /srv/debomatic/incoming/trim-galore_0.6.10-1.dsc Machine Architecture: amd64 Package: trim-galore Package-Time: 27 Source-Version: 0.6.10-1 Space: 88160 Status: successful Version: 0.6.10-1 -------------------------------------------------------------------------------- Finished at 2024-06-05T11:49:55Z Build needed 00:00:27, 88160k disk space