0s autopkgtest [09:32:46]: starting date and time: 2024-03-23 09:32:46+0000 0s autopkgtest [09:32:46]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [09:32:46]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.k6c6khuw/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:samtools,src:curl,src:gnutls28,src:htslib,src:libpsl,src:nettle,src:openssl --apt-upgrade stacks --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=samtools/1.19.2-1build1 curl/8.5.0-2ubuntu7 gnutls28/3.8.3-1.1ubuntu2 htslib/1.19+ds-1.1build2 libpsl/0.21.2-1.1 nettle/3.9.1-2.2 openssl/3.0.13-0ubuntu2' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos02-s390x-22.secgroup --name adt-noble-s390x-stacks-20240323-093246-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 119s autopkgtest [09:34:45]: testbed dpkg architecture: s390x 119s autopkgtest [09:34:45]: testbed apt version: 2.7.12 119s autopkgtest [09:34:45]: @@@@@@@@@@@@@@@@@@@@ test bed setup 120s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 120s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 120s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 120s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 120s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [4029 kB] 122s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main s390x Packages [651 kB] 122s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main s390x c-n-f Metadata [3032 B] 122s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x Packages [1372 B] 122s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted s390x c-n-f Metadata [116 B] 122s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x Packages [4144 kB] 122s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe s390x c-n-f Metadata [7292 B] 122s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x Packages [46.8 kB] 122s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse s390x c-n-f Metadata [116 B] 124s Fetched 9558 kB in 4s (2676 kB/s) 124s Reading package lists... 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Calculating upgrade... 127s The following packages will be REMOVED: 127s libssl3 127s The following NEW packages will be installed: 127s libssl3t64 127s The following packages have been kept back: 127s curl 127s The following packages will be upgraded: 127s libbsd0 libc-bin libc6 locales openssl 127s 5 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 127s Need to get 10.5 MB of archives. 127s After this operation, 241 kB of additional disk space will be used. 127s Get:1 http://ftpmaster.internal/ubuntu noble/main s390x libc6 s390x 2.39-0ubuntu6 [2847 kB] 128s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libc-bin s390x 2.39-0ubuntu6 [654 kB] 128s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/main s390x openssl s390x 3.0.13-0ubuntu2 [1010 kB] 128s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/main s390x libssl3t64 s390x 3.0.13-0ubuntu2 [1675 kB] 128s Get:5 http://ftpmaster.internal/ubuntu noble/main s390x libbsd0 s390x 0.12.1-1 [46.7 kB] 128s Get:6 http://ftpmaster.internal/ubuntu noble/main s390x locales all 2.39-0ubuntu6 [4232 kB] 128s Preconfiguring packages ... 128s Fetched 10.5 MB in 1s (10.7 MB/s) 128s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 128s Preparing to unpack .../libc6_2.39-0ubuntu6_s390x.deb ... 129s Unpacking libc6:s390x (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 129s Setting up libc6:s390x (2.39-0ubuntu6) ... 129s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 129s Preparing to unpack .../libc-bin_2.39-0ubuntu6_s390x.deb ... 129s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 129s Setting up libc-bin (2.39-0ubuntu6) ... 129s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 129s Preparing to unpack .../openssl_3.0.13-0ubuntu2_s390x.deb ... 129s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 129s dpkg: libssl3:s390x: dependency problems, but removing anyway as you requested: 129s wget depends on libssl3 (>= 3.0.0). 129s tnftp depends on libssl3 (>= 3.0.0). 129s tcpdump depends on libssl3 (>= 3.0.0). 129s systemd-resolved depends on libssl3 (>= 3.0.0). 129s systemd depends on libssl3 (>= 3.0.0). 129s sudo depends on libssl3 (>= 3.0.0). 129s s390-tools depends on libssl3 (>= 3.0.0). 129s rsync depends on libssl3 (>= 3.0.0). 129s python3-cryptography depends on libssl3 (>= 3.0.0). 129s openssh-server depends on libssl3 (>= 3.0.10). 129s openssh-client depends on libssl3 (>= 3.0.10). 129s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 129s libsystemd-shared:s390x depends on libssl3 (>= 3.0.0). 129s libssh-4:s390x depends on libssl3 (>= 3.0.0). 129s libsasl2-modules:s390x depends on libssl3 (>= 3.0.0). 129s libsasl2-2:s390x depends on libssl3 (>= 3.0.0). 129s libpython3.12-minimal:s390x depends on libssl3 (>= 3.0.0). 129s libpython3.11-minimal:s390x depends on libssl3 (>= 3.0.0). 129s libnvme1 depends on libssl3 (>= 3.0.0). 129s libkrb5-3:s390x depends on libssl3 (>= 3.0.0). 129s libkmod2:s390x depends on libssl3 (>= 3.0.0). 129s libfido2-1:s390x depends on libssl3 (>= 3.0.0). 129s libcurl4:s390x depends on libssl3 (>= 3.0.0). 129s libcryptsetup12:s390x depends on libssl3 (>= 3.0.0). 129s kmod depends on libssl3 (>= 3.0.0). 129s dhcpcd-base depends on libssl3 (>= 3.0.0). 129s bind9-libs:s390x depends on libssl3 (>= 3.0.0). 129s 129s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52170 files and directories currently installed.) 129s Removing libssl3:s390x (3.0.10-1ubuntu4) ... 129s Selecting previously unselected package libssl3t64:s390x. 129s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52159 files and directories currently installed.) 129s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_s390x.deb ... 129s Unpacking libssl3t64:s390x (3.0.13-0ubuntu2) ... 130s Preparing to unpack .../libbsd0_0.12.1-1_s390x.deb ... 130s Unpacking libbsd0:s390x (0.12.1-1) over (0.11.8-1) ... 130s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 130s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 130s Setting up libssl3t64:s390x (3.0.13-0ubuntu2) ... 130s Setting up locales (2.39-0ubuntu6) ... 130s Generating locales (this might take a while)... 132s en_US.UTF-8... done 132s Generation complete. 132s Setting up openssl (3.0.13-0ubuntu2) ... 132s Setting up libbsd0:s390x (0.12.1-1) ... 132s Processing triggers for man-db (2.12.0-3) ... 132s Processing triggers for libc-bin (2.39-0ubuntu6) ... 133s Reading package lists... 133s Building dependency tree... 133s Reading state information... 133s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 133s Unknown architecture, assuming PC-style ttyS0 133s sh: Attempting to set up Debian/Ubuntu apt sources automatically 133s sh: Distribution appears to be Ubuntu 134s Reading package lists... 134s Building dependency tree... 134s Reading state information... 135s eatmydata is already the newest version (131-1). 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s dbus is already the newest version (1.14.10-4ubuntu1). 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 135s Reading package lists... 135s Building dependency tree... 135s Reading state information... 135s rng-tools-debian is already the newest version (2.4). 135s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 136s Reading package lists... 136s Building dependency tree... 136s Reading state information... 136s The following packages will be REMOVED: 136s cloud-init* python3-configobj* python3-debconf* 136s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 136s After this operation, 3256 kB disk space will be freed. 136s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 52172 files and directories currently installed.) 136s Removing cloud-init (24.1.2-0ubuntu1) ... 136s Removing python3-configobj (5.0.8-3) ... 137s Removing python3-debconf (1.5.86) ... 137s Processing triggers for man-db (2.12.0-3) ... 137s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51783 files and directories currently installed.) 137s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 137s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 137s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 137s invoke-rc.d: policy-rc.d denied execution of try-restart. 138s Reading package lists... 138s Building dependency tree... 138s Reading state information... 138s linux-generic is already the newest version (6.8.0-11.11+1). 138s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 138s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 138s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 138s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 140s Reading package lists... 140s Reading package lists... 140s Building dependency tree... 140s Reading state information... 140s Calculating upgrade... 140s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 141s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 141s autopkgtest [09:35:07]: rebooting testbed after setup commands that affected boot 158s autopkgtest [09:35:24]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP Tue Feb 13 23:45:46 UTC 2024 161s autopkgtest [09:35:27]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 163s Get:1 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (dsc) [2041 B] 163s Get:2 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (tar) [339 kB] 163s Get:3 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (diff) [12.1 kB] 163s gpgv: Signature made Tue Jan 23 12:37:41 2024 UTC 163s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 163s gpgv: Can't check signature: No public key 163s dpkg-source: warning: cannot verify inline signature for ./stacks_2.66+dfsg-1.dsc: no acceptable signature found 163s autopkgtest [09:35:29]: testing package stacks version 2.66+dfsg-1 163s autopkgtest [09:35:29]: build not needed 164s autopkgtest [09:35:30]: test run-unit-test: preparing testbed 166s Reading package lists... 166s Building dependency tree... 166s Reading state information... 166s Starting pkgProblemResolver with broken count: 0 166s Starting 2 pkgProblemResolver with broken count: 0 166s Done 166s The following additional packages will be installed: 166s libdbi-perl libdeflate0 libgomp1 libhts3 libhtscodecs2 samtools stacks 166s Suggested packages: 166s libclone-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl cwltool 166s gdb 166s Recommended packages: 166s libspreadsheet-writeexcel-perl littler 167s The following NEW packages will be installed: 167s autopkgtest-satdep libdbi-perl libdeflate0 libgomp1 libhts3 libhtscodecs2 167s samtools stacks 167s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 167s Need to get 3223 kB/3224 kB of archives. 167s After this operation, 9158 kB of additional disk space will be used. 167s Get:1 /tmp/autopkgtest.66wUmt/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [704 B] 167s Get:2 http://ftpmaster.internal/ubuntu noble/main s390x libdbi-perl s390x 1.643-4build1 [724 kB] 167s Get:3 http://ftpmaster.internal/ubuntu noble/main s390x libdeflate0 s390x 1.19-1 [46.0 kB] 167s Get:4 http://ftpmaster.internal/ubuntu noble/main s390x libgomp1 s390x 14-20240303-1ubuntu1 [151 kB] 167s Get:5 http://ftpmaster.internal/ubuntu noble/universe s390x libhtscodecs2 s390x 1.6.0-1 [87.2 kB] 167s Get:6 http://ftpmaster.internal/ubuntu noble/universe s390x libhts3 s390x 1.18+ds-1 [463 kB] 167s Get:7 http://ftpmaster.internal/ubuntu noble/universe s390x samtools s390x 1.19.2-1 [613 kB] 167s Get:8 http://ftpmaster.internal/ubuntu noble/universe s390x stacks s390x 2.66+dfsg-1 [1138 kB] 168s Fetched 3223 kB in 1s (4140 kB/s) 168s Selecting previously unselected package libdbi-perl:s390x. 168s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 51728 files and directories currently installed.) 168s Preparing to unpack .../0-libdbi-perl_1.643-4build1_s390x.deb ... 168s Unpacking libdbi-perl:s390x (1.643-4build1) ... 168s Selecting previously unselected package libdeflate0:s390x. 168s Preparing to unpack .../1-libdeflate0_1.19-1_s390x.deb ... 168s Unpacking libdeflate0:s390x (1.19-1) ... 168s Selecting previously unselected package libgomp1:s390x. 168s Preparing to unpack .../2-libgomp1_14-20240303-1ubuntu1_s390x.deb ... 168s Unpacking libgomp1:s390x (14-20240303-1ubuntu1) ... 168s Selecting previously unselected package libhtscodecs2:s390x. 168s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_s390x.deb ... 168s Unpacking libhtscodecs2:s390x (1.6.0-1) ... 168s Selecting previously unselected package libhts3:s390x. 168s Preparing to unpack .../4-libhts3_1.18+ds-1_s390x.deb ... 168s Unpacking libhts3:s390x (1.18+ds-1) ... 168s Selecting previously unselected package samtools. 168s Preparing to unpack .../5-samtools_1.19.2-1_s390x.deb ... 168s Unpacking samtools (1.19.2-1) ... 168s Selecting previously unselected package stacks. 168s Preparing to unpack .../6-stacks_2.66+dfsg-1_s390x.deb ... 168s Unpacking stacks (2.66+dfsg-1) ... 168s Selecting previously unselected package autopkgtest-satdep. 168s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 168s Unpacking autopkgtest-satdep (0) ... 168s Setting up libhtscodecs2:s390x (1.6.0-1) ... 168s Setting up libdeflate0:s390x (1.19-1) ... 168s Setting up libgomp1:s390x (14-20240303-1ubuntu1) ... 168s Setting up libdbi-perl:s390x (1.643-4build1) ... 168s Setting up libhts3:s390x (1.18+ds-1) ... 168s Setting up samtools (1.19.2-1) ... 168s Setting up stacks (2.66+dfsg-1) ... 168s Setting up autopkgtest-satdep (0) ... 168s Processing triggers for man-db (2.12.0-3) ... 168s Processing triggers for libc-bin (2.39-0ubuntu6) ... 171s (Reading database ... 52043 files and directories currently installed.) 171s Removing autopkgtest-satdep (0) ... 171s autopkgtest [09:35:37]: test run-unit-test: [----------------------- 171s Stacks - a pipeline for building loci from short-read sequences 171s v2.66+dfsg http://creskolab.uoregon.edu/stacks/ 171s 171s This is the Stacks wrapper script for Debian. Usage: 171s stacks 171s 171s Programs available are: 171s clone_filter ref_map 171s cstacks sstacks 171s denovo_map stacks-dist-extract 171s gstacks stacks-gdb 171s kmer_filter stacks-integrate-alignments 171s phasedstacks stacks-samtools-tview 171s populations tsv2bam 171s process_radtags ustacks 171s process_shortreads 171s 171s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 171s 171s clone_filter 2.66 171s clone_filter [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -o out_dir [-i type] [-y type] [-D] [-h] 171s f: path to the input file if processing single-end sequences. 171s p: path to a directory of files. 171s P: files contained within directory specified by '-p' are paired. 171s 1: first input file in a set of paired-end sequences. 171s 2: second input file in a set of paired-end sequences. 171s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 171s o: path to output the processed files. 171s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 171s D: capture discarded reads to a file. 171s h: display this help message. 171s --oligo-len-1 len: length of the single-end oligo sequence in data set. 171s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 171s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 171s 171s Oligo sequence options: 171s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 171s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 171s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 171s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 171s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 171s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 171s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 171s --index-inline: random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data). 171s 171s cstacks 2.66 171s cstacks -P in_dir -M popmap [-n num_mismatches] [-p num_threads] 171s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-p num_threads] 171s 171s -P,--in-path: path to the directory containing Stacks files. 171s -M,--popmap: path to a population map file. 171s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 171s -p,--threads: enable parallel execution with num_threads threads. 171s -s: sample prefix from which to load loci into the catalog. 171s -o,--outpath: output path to write results. 171s -c,--catalog : add to an existing catalog. 171s 171s Gapped assembly options: 171s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 171s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 171s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 171s 171s Advanced options: 171s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 171s --report-mmatches: report query loci that match more than one catalog locus. 171s denovo_map.pl 2.66 171s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 171s 171s Input/Output files: 171s --samples: path to the directory containing the reads files for each sample. 171s --popmap: path to a population map file (format is " TAB ", one sample per line). 171s -o,--out-path: path to an output directory. 171s 171s General options: 171s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 171s -T, --threads: the number of threads/CPUs to use (default: 1). 171s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 171s --resume: resume executing the pipeline from a previous run. 171s 171s Stack assembly options: 171s -M: number of mismatches allowed between stacks within individuals (for ustacks). 171s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 171s 171s SNP model options: 171s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 171s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 171s 171s Paired-end options: 171s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 171s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 171s the same insert length. 171s 171s Population filtering options: 171s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 171s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 171s 171s For large datasets: 171s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 171s 171s Miscellaneous: 171s --time-components (for benchmarking) 171s gstacks 2.66 171s 171s De novo mode: 171s gstacks -P stacks_dir -M popmap 171s 171s -P: input directory containing '*.matches.bam' files created by the 171s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 171s 171s Reference-based mode: 171s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 171s gstacks -B bam_file [-B ...] -O out_dir 171s 171s -I: input directory containing BAM files 171s -S: with -I/-M, suffix to use to build BAM file names: by default this 171s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 171s -B: input BAM file(s) 171s 171s The input BAM file(s) must be sorted by coordinate. 171s With -B, records must be assigned to samples using BAM "reads groups" 171s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 171s must be consistent if repeated different files. Note that with -I, read 171s groups are unneeded and ignored. 171s 171s For both modes: 171s -M: path to a population map giving the list of samples 171s -O: output directory (default: none with -B; with -P same as the input 171s directory) 171s -t,--threads: number of threads to use (default: 1) 171s 171s SNP Model options: 171s --model: model to use to call variants and genotypes; one of 171s marukilow (default), marukihigh, or snp 171s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 171s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 171s 171s Paired-end options: 171s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 171s have the same insert length (implies --rm-unpaired-reads) 171s --rm-unpaired-reads: discard unpaired reads 171s --ignore-pe-reads: ignore paired-end reads even if present in the input 171s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 171s 171s Advanced options: 171s (De novo mode) 171s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 171s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 171s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 171s --write-alignments: save read alignments (heavy BAM files) 171s 171s (Reference-based mode) 171s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 171s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 171s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 171s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 171s 171s --details: write a heavier output 171s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 171s iterate over when building the graph of allele cooccurrences for 171s SNP phasing (default: 1,2) 171s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 171s genotypes during phasing 171s 171s kmer_filter 2.66 171s kmer_filter [-f in_file_1 [-f in_file_2...] | -p in_dir] [-1 pair_1 -2 pair_2 [-1 pair_1...]] -o out_dir [-i type] [-y type] [-D] [-h] 171s f: path to the input file if processing single-end seqeunces. 171s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 171s p: path to a directory of files (for single-end files only). 171s 1: specify the first in a pair of files to be processed together. 171s 2: specify the second in a pair of files to be processed together. 171s o: path to output the processed files. 171s y: output type, either 'fastq' or 'fasta' (default fastq). 171s D: capture discarded reads to a file. 171s h: display this help message. 171s 171s Filtering options: 171s --rare: turn on filtering based on rare k-mers. 171s --abundant: turn on filtering based on abundant k-mers. 171s --k-len : specify k-mer size (default 15). 171s 171s Advanced filtering options: 171s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 171s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 171s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 171s 171s Normalize data: 171s --normalize : normalize read depth according to k-mer coverage. 171s 171s Characterizing K-mers: 171s --write-k-freq: write kmers along with their frequency of occurrence and exit. 171s --k-dist: print k-mer frequency distribution and exit. 171s 171s Advanced input options: 171s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 171s 171s phasedstacks 2.66 171s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 171s b: Stacks batch ID. 171s P: path to the phased output files. 171s S: path to the Stacks output files. 171s t: input file type. Supported types: fastphase, and beagle. 171s p: number of processes to run in parallel sections of code. 171s M: path to the population map, a tab separated file describing which individuals belong in which population. 171s v: print program version. 171s h: display this help message. 171s --haplotypes: data were phased as RAD locus haplotypes. 171s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 171s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 171s 171s Filtering options: 171s --skip-zeros: do not include D' values of zero in the D' output. 171s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 171s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 171s 171s populations 2.66 171s Usage: 171s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 171s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 171s 171s -P,--in-path: path to a directory containing Stacks output files. 171s -V,--in-vcf: path to a standalone input VCF file. 171s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 171s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 171s -t,--threads: number of threads to run in parallel sections of code. 171s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 171s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 171s 171s Data Filtering: 171s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 171s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 171s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 171s -H,--filter-haplotype-wise: apply the above filters haplotype wise 171s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 171s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 171s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 171s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 171s 171s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 171s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 171s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 171s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 171s 171s Locus stats: 171s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 171s 171s Fstats: 171s --fstats: enable SNP and haplotype-based F statistics. 171s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 171s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 171s 171s Kernel-smoothing algorithm: 171s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 171s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 171s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 171s (Note: turning on smoothing implies --ordered-export.) 171s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 171s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 171s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 171s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 171s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 171s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 171s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 171s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 171s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 171s 171s File output options: 171s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 171s --fasta-loci: output locus consensus sequences in FASTA format. 171s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 171s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 171s --vcf-all: output all sites in Variant Call Format (VCF). 171s --genepop: output SNPs and haplotypes in GenePop format. 171s --structure: output results in Structure format. 171s --radpainter: output results in fineRADstructure/RADpainter format. 171s --plink: output genotypes in PLINK format. 171s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 171s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 171s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 171s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 171s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 171s --gtf: output locus positions in a GTF annotation file. 171s --no-hap-exports: omit haplotype outputs. 171s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 171s 171s Genetic map output options (population map must specify a genetic cross): 171s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 171s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 171s 171s Additional options: 171s -h,--help: display this help message. 171s -v,--version: print program version. 171s --verbose: turn on additional logging. 171s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 171s process_radtags 2.66 171s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 171s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 171s process_radtags --in-path in_dir [--paired] [--barcodes barcode_file] --out-path out_dir --renz-1 enz [--renz-2 enz] [--threads num] [-c] [-q] [-r] [-t len] 171s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 171s 171s -p,--in-path: path to a directory of files. 171s -P,--paired: files contained within the directory are paired. 171s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 171s -i,--in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 171s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 171s -o,--out-path: path to output the processed files. 171s -f: path to the input file if processing single-end sequences. 171s -1: first input file in a set of paired-end sequences. 171s -2: second input file in a set of paired-end sequences. 171s --threads: number of threads to run. 171s -c,--clean: clean data, remove any read with an uncalled base ('N'). 171s -q,--quality: discard reads with low quality (phred) scores. 171s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 171s -t,--truncate: truncate final read length to this value. 171s -D,--discards: capture discarded reads to a file. 171s -y,--out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 171s 171s Barcode options: 171s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 171s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 171s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 171s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 171s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 171s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 171s --index-inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data). 171s 171s Restriction enzyme options: 171s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 171s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 171s Currently supported enzymes include: 171s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 171s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 171s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 171s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 171s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 171s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 171s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 171s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 171s 171s Protocol-specific options: 171s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 171s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 171s 171s Adapter options: 171s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 171s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 171s --adapter-mm : number of mismatches allowed in the adapter sequence. 171s 171s Output options: 171s --retain-header: retain unmodified FASTQ headers in the output. 171s --merge: if no barcodes are specified, merge all input files into a single output file. 171s 171s Advanced options: 171s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 171s --disable-rad-check: disable checking if the RAD cut site is intact. 171s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 171s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 171s --score-limit: set the phred score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 171s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 171s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 171s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 171s process_shortreads 2.66 171s process_shortreads [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir [-i type] [-y type] [-c] [-q] [-r] [-E encoding] [-t len] [-D] [-w size] [-s lim] [-h] 171s f: path to the input file if processing single-end seqeunces. 171s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 171s p: path to a directory of single-end Illumina files. 171s 1: first input file in a set of paired-end sequences. 171s 2: second input file in a set of paired-end sequences. 171s P: specify that input is paired (for use with '-p'). 171s I: specify that the paired-end reads are interleaved in single files. 171s o: path to output the processed files. 171s y: output type, either 'fastq' or 'fasta' (default gzfastq). 171s b: a list of barcodes for this run. 171s c: clean data, remove any read with an uncalled base. 171s q: discard reads with low quality scores. 171s r: rescue barcodes. 171s t: truncate final read length to this value. 171s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 171s D: capture discarded reads to a file. 171s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 171s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 171s h: display this help message. 171s 171s Barcode options: 171s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 171s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 171s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 171s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 171s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 171s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 171s --index-inline: barcode occurs in FASTQ header (Illumina i5 or i7 read) and is inline with single-end sequence (for single-end data) on paired-end read (for paired-end data). 171s 171s Adapter options: 171s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 171s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 171s --adapter-mm : number of mismatches allowed in the adapter sequence. 171s 171s Output options: 171s --retain-header: retain unmodified FASTQ headers in the output. 171s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 171s 171s Advanced options: 171s --no-read-trimming: do not trim low quality reads, just discard them. 171s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 171s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 171s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 171s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 171s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 171s ref_map.pl 2.66 171s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 171s 171s Input/Output files: 171s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 171s --popmap: path to a population map file (format is " TAB ", one sample per line). 171s -s: spacer for file names: by default this is empty and the program looks for files 171s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 171s named 'SAMPLE_NAME.SPACER.bam'. 171s -o,--out-path: path to an output directory. 171s 171s General options: 171s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 171s -T: the number of threads/CPUs to use (default: 1). 171s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 171s that would be executed. 171s 171s SNP model options: 171s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 171s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 171s 171s Paired-end options: 171s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 171s the same insert length. 171s --ignore-pe-reads: ignore paired-end reads even if present in the input 171s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 171s 171s Population filtering options: 171s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 171s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 171s 171s Miscellaneous: 171s --time-components (for benchmarking) 171s sstacks 2.66 171s sstacks -P dir -M popmap [-p n_threads] 171s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads] 171s -P,--in-path: path to the directory containing Stacks files. 171s -M,--popmap: path to a population map file from which to take sample names. 171s -s,--sample: filename prefix from which to load sample loci. 171s -c,--catalog: path to the catalog. 171s -p,--threads: enable parallel execution with n_threads threads. 171s -o,--out-path: output path to write results. 171s -x: don't verify haplotype of matching locus. 171s 171s Gapped assembly options: 171s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 171s usage: 171s stacks-dist-extract logfile [section] 171s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 171s cat logfile | stacks-dist-extract [--pretty] [--section section] 171s 171s Export a paricular section of a Stacks log or distribs file. If you supply a 171s log path alone, stacks-dist-extract will print the available sections to 171s output. The log file can also be supplied via stdin. 171s 171s options: 171s -h, --help show this help message and exit 171s -p, --pretty Output data as a table with columns lined up. 171s -o path, --out-path path 171s Path to output file. 171s -s section, --section section 171s Name of section to output from the log file. 171s Usage: 171s stacks-gdb PROGRAM ARGUMENTS 171s 171s e.g. 171s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 171s 171s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 171s case of a crash it will print additional information, helping us in fixing the 171s crash. 171s 171s This utility requires GDB, the GNU Debugger, to be installed on the system where 171s Stacks is run. You can check whether this is the case by just typing: 171s 171s gdb --version 171s 171s at the command prompt. Note that you may need to load the corresponding module. 171s GDB is standard scientific software, but may not be installed on some systems. 171s For further information please contact the administrators of your system; 171s trying to install GDB without administrator priviledges is not recommended. 171s 171s For questions please contact us, e.g. at stacks-users@googlegroups.com 171s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 171s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 171s [--version] 171s 171s Extracts the coordinates of the RAD loci from the given BAM file into a 171s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 171s 'catalog.calls' files so that they include the genomic coordinates given in 171s the input BAM file. 171s 171s options: 171s -h, --help show this help message and exit 171s -P path, --in-path path 171s Path to a directory containing Stacks ouput files. 171s -B path, --bam-path path 171s Path to a SAM or BAM file containing alignment of de 171s novo catalog loci to a reference genome. 171s -O path, --out-path path 171s Path to write the integrated ouput files. 171s -q MIN_MAPQ, --min_mapq MIN_MAPQ 171s Minimum mapping quality as listed in the BAM file 171s (default 20). 171s -a MIN_ALNCOV, --min_alncov MIN_ALNCOV 171s Minimum fraction of the de novo catalog locus that 171s must participate in the alignment (default 0.6). 171s -p MIN_PCTID, --min_pctid MIN_PCTID 171s Minimum BLAST-style percent identity of the largest 171s alignment fragment for a de novo catalog locus 171s (default 0.6). 171s --verbose Provide verbose output. 171s --version show program's version number and exit 171s usage: 171s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 171s 171s Displays the read alignments of the given sample for the given locus, in text 171s format, to the standard output. Requires gstacks to have been run with the 171s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 171s tsv2bam 2.66 171s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 171s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 171s 171s -P,--in-dir: input directory. 171s -M,--popmap: population map. 171s -s,--sample: name of one sample. 171s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 171s -t: number of threads to use (default: 1). 171s 171s ustacks 2.66 171s ustacks -f file_path -o path [-M max_dist] [-m min_cov] [-p num_threads] 171s f: input file path. 171s o: output path to write results. 171s M: Maximum distance (in nucleotides) allowed between stacks (default 2). 171s m: Minimum depth of coverage required to create a stack (default 3). 171s N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 171s p: enable parallel execution with num_threads threads. 171s t: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 171s --name: a name for the sample (default: input file name minus the suffix). 171s R: retain unused reads. 171s H: disable calling haplotypes from secondary reads. 171s 171s Stack assembly options: 171s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 171s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 171s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 171s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 171s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 171s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 171s 171s Gapped assembly options: 171s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 171s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 171s 171s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 171s Model options: 171s --model-type: either 'snp' (default), 'bounded', or 'fixed' 171s For the SNP or Bounded SNP model: 171s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 171s For the Bounded SNP model: 171s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 171s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 171s For the Fixed model: 171s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 171s 171s h: display this help message. 172s autopkgtest [09:35:38]: test run-unit-test: -----------------------] 172s autopkgtest [09:35:38]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 172s run-unit-test PASS (superficial) 173s autopkgtest [09:35:39]: @@@@@@@@@@@@@@@@@@@@ summary 173s run-unit-test PASS (superficial) 184s Creating nova instance adt-noble-s390x-stacks-20240323-093246-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-s390x-server-20240322.img (UUID c8671f9a-0e89-48e3-af4f-3c79b89294e8)...