Start: 2023-02-05 17:58:07 GMT [jessie] Package: fastaq Version: 1.5.0-1 Installed-Size: 169 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-nose, python3:any (>= 3.3.2-2~), python3 Description: FASTA and FASTQ file manipulation tools Homepage: https://github.com/sanger-pathogens/Fastaq Description-md5: b0a4048682c8002d3ec3d2b1b24e6aa6 Section: science Priority: optional Filename: pool/main/f/fastaq/fastaq_1.5.0-1_all.deb Size: 49952 MD5sum: 56a418024924ec583007b70dc71e9ffb SHA1: eca47e5f5bab2f4b1ebe52b3504061792034e4a2 SHA256: 5bc097f2c4a4b9b7f5f63c5962a2c1b87e74049862e6354a5fa0e080d67cfa58 [stretch] Package: fastaq Version: 3.14.0-1 Installed-Size: 190 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any (>= 3.3.2-2~), python3-pkg-resources, samtools Description: FASTA and FASTQ file manipulation tools Homepage: https://github.com/sanger-pathogens/Fastaq Description-md5: 87737379b65cd806e7ab8b37901b7e08 Tag: biology::format:fasta, biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, scope::utility, use::analysing, use::calculating, use::checking, use::converting, use::filtering, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/f/fastaq/fastaq_3.14.0-1_all.deb Size: 46632 MD5sum: 98999fd8b7ab873d2289438fed88bb25 SHA256: 5df0b3b313b9265237d84c7442260138f26a82666d5f1cf38dce4c6bfdc63b18 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-recommends --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz -d jessie -d stretch -B /srv/piuparts.debian.org/slave/refchroot/jessie2Xstretch-rcmd/reference-chroot-metadata.dat --apt fastaq=3.14.0-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-recommends --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz -d jessie -d stretch -B /srv/piuparts.debian.org/slave/refchroot/jessie2Xstretch-rcmd/reference-chroot-metadata.dat --apt fastaq=3.14.0-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpqnfecxas 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpqnfecxas 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/jessie_amd64.tar.gz'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/proc'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/proc'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/pts'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/pts'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/ptmx'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/ptmx'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/console'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/console'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/shm'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/shm'] 0m1.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ jessie main 0m1.5s DEBUG: Created policy-rc.d and chmodded it. 0m1.5s DEBUG: Created resolv.conf. 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpqnfecxas/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-get', 'update'] 0m3.1s DUMP: Ign http://deb.debian.org jessie InRelease Hit http://deb.debian.org jessie Release.gpg Hit http://deb.debian.org jessie Release Ign http://deb.debian.org jessie Release Hit http://deb.debian.org jessie/main Translation-en Hit http://deb.debian.org jessie/main amd64 Packages Reading package lists... W: GPG error: http://deb.debian.org jessie Release: The following signatures were invalid: KEYEXPIRED 1668891673 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-get', 'update'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DUMP: Reading package lists... Building dependency tree... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-get', '-yf', 'dist-upgrade'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.5s DUMP: c58dd1ad19dd97acb5ff8b7cd65de431 - 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.5s INFO: Running scripts post_setup 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_minimize'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_minimize'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.0s DUMP: install ok installed acl acl 2.2.52-2 install ok installed adduser adduser 3.113+nmu3 install ok installed apt apt 1.0.9.8.4 install ok installed base-files base-files 8+deb8u11 install ok installed base-passwd base-passwd 3.5.37 install ok installed bash bash 4.3-11+deb8u1 install ok installed bsdutils bsdutils 1:2.25.2-6 install ok installed coreutils coreutils 8.23-4 install ok installed dash dash 0.5.7-4+b1 install ok installed debconf debconf 1.5.56+deb8u1 install ok installed debconf-i18n debconf-i18n 1.5.56+deb8u1 install ok installed debian-archive-keyring debian-archive-keyring 2017.5~deb8u1 install ok installed debianutils debianutils 4.4+b1 install ok installed diffutils diffutils 1:3.3-1+b1 install ok installed dmsetup dmsetup 2:1.02.90-2.2+deb8u1 install ok installed dpkg dpkg 1.17.27 install ok installed e2fslibs:amd64 e2fslibs 1.42.12-2+b1 install ok installed e2fsprogs e2fsprogs 1.42.12-2+b1 install ok installed findutils findutils 4.4.2-9+b1 install ok installed gcc-4.9-base:amd64 gcc-4.9-base 4.9.2-10+deb8u1 install ok installed gnupg gnupg 1.4.18-7+deb8u5 install ok installed gpgv gpgv 1.4.18-7+deb8u5 install ok installed grep grep 2.20-4.1 install ok installed gzip gzip 1.6-4 install ok installed hostname hostname 3.15 install ok installed init init 1.22 install ok installed initscripts initscripts 2.88dsf-59 install ok installed insserv insserv 1.14.0-5 install ok installed libacl1:amd64 libacl1 2.2.52-2 install ok installed libapt-pkg4.12:amd64 libapt-pkg4.12 1.0.9.8.4 install ok installed libattr1:amd64 libattr1 1:2.4.47-2 install ok installed libaudit-common libaudit-common 1:2.4-1 install ok installed libaudit1:amd64 libaudit1 1:2.4-1+b1 install ok installed libblkid1:amd64 libblkid1 2.25.2-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-7+b3 install ok installed libc-bin libc-bin 2.19-18+deb8u10 install ok installed libc6:amd64 libc6 2.19-18+deb8u10 install ok installed libcap2:amd64 libcap2 1:2.24-8 install ok installed libcap2-bin libcap2-bin 1:2.24-8 install ok installed libcomerr2:amd64 libcomerr2 1.42.12-2+b1 install ok installed libcryptsetup4:amd64 libcryptsetup4 2:1.6.6-5 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-9+deb8u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.192 install ok installed libdevmapper1.02.1:amd64 libdevmapper1.02.1 2:1.02.90-2.2+deb8u1 install ok installed libgcc1:amd64 libgcc1 1:4.9.2-10+deb8u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.6.3-2+deb8u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.17-3 install ok installed libkmod2:amd64 libkmod2 18-3 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.05-8+b1 install ok installed liblzma5:amd64 liblzma5 5.1.1alpha+20120614-2+b3 install ok installed libmount1:amd64 libmount1 2.25.2-6 install ok installed libncurses5:amd64 libncurses5 5.9+20140913-1+deb8u3 install ok installed libncursesw5:amd64 libncursesw5 5.9+20140913-1+deb8u3 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.1+deb8u2+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.1+deb8u2+b1 install ok installed libpam-runtime libpam-runtime 1.1.8-3.1+deb8u2 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.1+deb8u2+b1 install ok installed libpcre3:amd64 libpcre3 2:8.35-3.3+deb8u4 install ok installed libprocps3:amd64 libprocps3 2:3.3.9-9+deb8u1 install ok installed libreadline6:amd64 libreadline6 6.3-8+b3 install ok installed libselinux1:amd64 libselinux1 2.3-2 install ok installed libsemanage-common libsemanage-common 2.3-1 install ok installed libsemanage1:amd64 libsemanage1 2.3-1+b1 install ok installed libsepol1:amd64 libsepol1 2.3-2 install ok installed libslang2:amd64 libslang2 2.3.0-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.25.2-6 install ok installed libss2:amd64 libss2 1.42.12-2+b1 install ok installed libstdc++6:amd64 libstdc++6 4.9.2-10+deb8u1 install ok installed libsystemd0:amd64 libsystemd0 215-17+deb8u7 install ok installed libtext-charwidth-perl libtext-charwidth-perl 0.04-7+b3 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5+b2 install ok installed libtext-wrapi18n-perl libtext-wrapi18n-perl 0.06-7 install ok installed libtinfo5:amd64 libtinfo5 5.9+20140913-1+deb8u3 install ok installed libudev1:amd64 libudev1 215-17+deb8u7 install ok installed libusb-0.1-4:amd64 libusb-0.1-4 2:0.1.12-25 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-3+b2 install ok installed libuuid1:amd64 libuuid1 2.25.2-6 install ok installed login login 1:4.2-3+deb8u4 install ok installed lsb-base lsb-base 4.1+Debian13+nmu1 install ok installed mawk mawk 1.3.3-17 install ok installed mount mount 2.25.2-6 install ok installed multiarch-support multiarch-support 2.19-18+deb8u10 install ok installed ncurses-base ncurses-base 5.9+20140913-1+deb8u3 install ok installed ncurses-bin ncurses-bin 5.9+20140913-1+deb8u3 install ok installed passwd passwd 1:4.2-3+deb8u4 install ok installed perl-base perl-base 5.20.2-3+deb8u11 install ok installed procps procps 2:3.3.9-9+deb8u1 install ok installed readline-common readline-common 6.3-8 install ok installed sed sed 4.2.2-4+deb8u1 install ok installed sensible-utils sensible-utils 0.0.9+deb8u1 install ok installed startpar startpar 0.59-3 install ok installed systemd systemd 215-17+deb8u7 install ok installed systemd-sysv systemd-sysv 215-17+deb8u7 install ok installed sysv-rc sysv-rc 2.88dsf-59 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59 install ok installed tar tar 1.27.1-2+deb8u1 install ok installed tzdata tzdata 2018e-0+deb8u1 install ok installed udev udev 215-17+deb8u7 install ok installed util-linux util-linux 2.25.2-6 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-2+b1 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/jessie2Xstretch-rcmd/reference-chroot-metadata.dat 0m4.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqnfecxas'] 0m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpqnfecxas'] 0m4.4s INFO: Running scripts is_testable 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s INFO: Running scripts pre_test 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_test_root_password'] 0m4.4s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_test_root_password'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-cache', 'show', '--no-all-versions', 'fastaq'] 0m4.4s DUMP: Package: fastaq Version: 1.5.0-1 Installed-Size: 169 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-nose, python3:any (>= 3.3.2-2~), python3 Description-en: FASTA and FASTQ file manipulation tools A collection of scripts that perform useful and common fasta/q manipulation tasks. . All scripts automatically detect whether the input is a FASTA or FASTQ file. . Input and output files can be gzipped. . fastaq_capillary_to_pairs - Given a fasta/q file of capillary reads, makes an interleaved file of read pairs . fastaq_chunker - Splits a multi fasta/q file into separate files. Splits sequences into chunks of a fixed size. . fastaq_count_sequences - Counts the number of sequences in a fasta/q file . fastaq_deinterleave - Deinterleaves fasta/q file, so that reads are written alternately between two output files . fastaq_enumerate_names - Renames sequences in a file, calling them 1,2,3... . fastaq_expand_nucleotides - Makes all combinations of sequences in input file by using all possibilities of redundant bases. e.g. ART could be AAT or AGT. . fastaq_extend_gaps - Extends the length of all gaps (and trims the start/end of sequences) in a fasta/q file. . fastaq_fasta_to_fastq - Given a fasta and qual file, makes a fastq file. . fastaq_filter - Filters a fasta/q file by sequence length and/or by name matching a regular expression. . fastaq_get_ids - Gets IDs from each sequence in a fasta or fastq file. . fastaq_get_seq_flanking_gaps - Gets the sequences either side of gaps in a fasta/q file. . fastaq_insert_or_delete_bases - Deletes or inserts bases at given position(s) from a fasta/q file. . fastaq_interleave - Interleaves two fasta/q files, so that reads are written alternately first/second in output file. . fastaq_long_read_simulate - Simulates long reads from a fasta/q file. Can optionally make insertions into the reads, like pacbio does. . fastaq_make_random_contigs - Makes a multi-fasta file of random sequences, all of the same length. Each base has equal chance of being A,C,G or T . fastaq_merge - Converts multi fasta/q file to single sequence file, preserving original order of sequences. . fastaq_replace_bases - Replaces all occurences of one letter with another in a fasta/q file. . fastaq_reverse_complement - Reverse complements all sequences in a fasta/q file . fastaq_scaffolds_to_contigs - Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input. . fastaq_search_for_seq - Searches for an exact match on a given string and its reverese complement, in every sequences of a fasta/q file. Case insensitive. Guaranteed to find all hits. . fastaq_sequence_trim - Trims sequences off the start of all sequences in a pair of fasta/q files, whenever there is a perfect match. Only keeps a read pair if both reads of the pair are at least a minimum length after any trimming. . fastaq_split_by_base_count - Splits a multi fasta/q file into separate files. Does not split sequences. Puts up to max_bases into each split file. The exception is that any sequence longer than max_bases is put into its own file. . fastaq_strip_illumina_suffix - Strips /1 or /2 off the end of every read name in a fasta/q file. . fastaq_to_fake_qual - Makes fake quality scores file from a fasta/q file. . fastaq_to_fasta - Converts sequence file to FASTA format. . fastaq_to_mira_xml - Creates an xml file from a fasta/q file of reads, for use with Mira assembler. . fastaq_to_orfs_gff - Writes a GFF file of open reading frames from a fasta/q file . fastaq_to_perfect_reads - Makes perfect paired end fastq reads from a fasta/q file, with insert sizes sampled from a normal distribution. Read orientation is innies. Output is an interleaved fastq file. . fastaq_to_quasr_primers_file - Converts a fasta/q file to QUASR primers format: just the sequence on each line and its reverse complement, tab separated. . fastaq_to_random_subset - Takes a random subset of reads from a fasta/q file and optionally the corresponding read from a mates file. Ouptut is interleaved if mates file given. . fastaq_to_tiling_bam - Takes a fasta/q file. Makes a BAM file containing perfect (unpaired) reads tiling the whole genome. . fastaq_to_unique_by_id - Removes duplicate sequences from a fasta/q file, based on their names. If the same name is found more than once, then the longest sequence is kept. Order of sequences is preserved in output. . fastaq_translate - Translates all sequences in a fasta or fastq file. Output is always fasta format . fastaq_trim_ends - Trims set number of bases off each sequence in a fasta/q file . fastaq_trim_Ns_at_end - Trims any Ns off each sequence in a fasta/q file. Does nothing to gaps in the middle, just trims the ends . A developer API is also provided by this package. There are plenty of examples in tasks.py Description-md5: b0a4048682c8002d3ec3d2b1b24e6aa6 Homepage: https://github.com/sanger-pathogens/Fastaq Section: science Priority: optional Filename: pool/main/f/fastaq/fastaq_1.5.0-1_all.deb Size: 49952 MD5sum: 56a418024924ec583007b70dc71e9ffb SHA1: eca47e5f5bab2f4b1ebe52b3504061792034e4a2 SHA256: 5bc097f2c4a4b9b7f5f63c5962a2c1b87e74049862e6354a5fa0e080d67cfa58 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-cache', 'show', '--no-all-versions', 'fastaq'] 0m4.4s INFO: apt-cache knows about the following packages: fastaq 0m4.4s INFO: Running scripts pre_install 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-cache', 'policy'] 0m4.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian/ jessie/main Translation-en 500 http://deb.debian.org/debian/ jessie/main amd64 Packages release v=8.11,o=Debian,a=oldoldstable,n=jessie,l=Debian,c=main origin deb.debian.org Pinned packages: 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-cache', 'policy'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-cache', 'policy', 'fastaq'] 0m4.5s DUMP: fastaq: Installed: (none) Candidate: 1.5.0-1 Version table: 1.5.0-1 0 500 http://deb.debian.org/debian/ jessie/main amd64 Packages 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-cache', 'policy', 'fastaq'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-get', '-y', 'install', 'fastaq'] 0m4.7s DUMP: Reading package lists... Building dependency tree... The following extra packages will be installed: dh-python file libexpat1 libffi6 libmagic1 libmpdec2 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsqlite3-0 libssl1.0.0 mime-support python3 python3-minimal python3-nose python3-pkg-resources python3.4 python3.4-minimal Suggested packages: python3-doc python3-tk python3-venv python-nose-doc python3-setuptools python3.4-venv python3.4-doc binutils binfmt-support The following NEW packages will be installed: dh-python fastaq file libexpat1 libffi6 libmagic1 libmpdec2 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsqlite3-0 libssl1.0.0 mime-support python3 python3-minimal python3-nose python3-pkg-resources python3.4 python3.4-minimal 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. Need to get 6800 kB of archives. After this operation, 27.6 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libssl1.0.0 libmagic1 libsqlite3-0 libexpat1 libffi6 libmpdec2 libpython3.4-minimal mime-support libpython3.4-stdlib python3.4-minimal file python3.4 python3-minimal libpython3-stdlib python3 dh-python python3-pkg-resources python3-nose fastaq E: There are problems and -y was used without --force-yes 0m4.7s ERROR: Command failed (status=100): ['chroot', '/srv/piuparts.debian.org/tmp/tmpqnfecxas', 'apt-get', '-y', 'install', 'fastaq'] Reading package lists... Building dependency tree... The following extra packages will be installed: dh-python file libexpat1 libffi6 libmagic1 libmpdec2 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsqlite3-0 libssl1.0.0 mime-support python3 python3-minimal python3-nose python3-pkg-resources python3.4 python3.4-minimal Suggested packages: python3-doc python3-tk python3-venv python-nose-doc python3-setuptools python3.4-venv python3.4-doc binutils binfmt-support The following NEW packages will be installed: dh-python fastaq file libexpat1 libffi6 libmagic1 libmpdec2 libpython3-stdlib libpython3.4-minimal libpython3.4-stdlib libsqlite3-0 libssl1.0.0 mime-support python3 python3-minimal python3-nose python3-pkg-resources python3.4 python3.4-minimal 0 upgraded, 19 newly installed, 0 to remove and 0 not upgraded. Need to get 6800 kB of archives. After this operation, 27.6 MB of additional disk space will be used. WARNING: The following packages cannot be authenticated! libssl1.0.0 libmagic1 libsqlite3-0 libexpat1 libffi6 libmpdec2 libpython3.4-minimal mime-support libpython3.4-stdlib python3.4-minimal file python3.4 python3-minimal libpython3-stdlib python3 dh-python python3-pkg-resources python3-nose fastaq E: There are problems and -y was used without --force-yes 0m5.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/shm'] 0m5.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/shm'] 0m5.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/console'] 0m5.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/console'] 0m5.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/ptmx'] 0m5.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/ptmx'] 0m5.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/pts'] 0m5.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/dev/pts'] 0m5.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/proc'] 0m5.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpqnfecxas/proc'] 0m5.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqnfecxas'] 0m5.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpqnfecxas'] 0m5.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpqnfecxas 0m5.1s ERROR: piuparts run ends. ret=1 End: 2023-02-05 17:58:12 GMT