0s autopkgtest [18:00:20]: starting date and time: 2024-03-24 18:00:20+0000 0s autopkgtest [18:00:20]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [18:00:20]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.2nx2om80/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-3@bos03-arm64-4.secgroup --name adt-noble-arm64-stacks-20240324-174632-juju-7f2275-prod-proposed-migration-environment-3 --image adt/ubuntu-noble-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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/ 76s autopkgtest [18:01:36]: testbed dpkg architecture: arm64 76s autopkgtest [18:01:36]: testbed apt version: 2.7.12 76s autopkgtest [18:01:36]: @@@@@@@@@@@@@@@@@@@@ test bed setup 77s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 77s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [496 kB] 77s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 77s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3986 kB] 78s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [57.3 kB] 78s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 Packages [710 kB] 78s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 c-n-f Metadata [3144 B] 78s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 Packages [33.7 kB] 78s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted arm64 c-n-f Metadata [116 B] 78s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 Packages [4364 kB] 78s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/universe arm64 c-n-f Metadata [8528 B] 78s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 Packages [70.1 kB] 78s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/multiverse arm64 c-n-f Metadata [116 B] 80s Fetched 9851 kB in 2s (5387 kB/s) 80s Reading package lists... 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 85s Calculating upgrade... 85s The following packages will be REMOVED: 85s libssl3 85s The following NEW packages will be installed: 85s libssl3t64 85s The following packages have been kept back: 85s curl 85s The following packages will be upgraded: 85s openssl 86s 1 upgraded, 1 newly installed, 1 to remove and 1 not upgraded. 86s Need to get 2777 kB of archives. 86s After this operation, 139 kB of additional disk space will be used. 86s Get:1 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 openssl arm64 3.0.13-0ubuntu2 [985 kB] 86s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main arm64 libssl3t64 arm64 3.0.13-0ubuntu2 [1793 kB] 87s Fetched 2777 kB in 1s (3695 kB/s) 87s (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 ... 74819 files and directories currently installed.) 87s Preparing to unpack .../openssl_3.0.13-0ubuntu2_arm64.deb ... 87s Unpacking openssl (3.0.13-0ubuntu2) over (3.0.10-1ubuntu4) ... 87s dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: 87s wget depends on libssl3 (>= 3.0.0). 87s u-boot-tools depends on libssl3 (>= 3.0.0). 87s tnftp depends on libssl3 (>= 3.0.0). 87s tcpdump depends on libssl3 (>= 3.0.0). 87s systemd-resolved depends on libssl3 (>= 3.0.0). 87s systemd depends on libssl3 (>= 3.0.0). 87s sudo depends on libssl3 (>= 3.0.0). 87s sbsigntool depends on libssl3 (>= 3.0.0). 87s rsync depends on libssl3 (>= 3.0.0). 87s python3-cryptography depends on libssl3 (>= 3.0.0). 87s openssh-server depends on libssl3 (>= 3.0.10). 87s openssh-client depends on libssl3 (>= 3.0.10). 87s mtd-utils depends on libssl3 (>= 3.0.0). 87s mokutil depends on libssl3 (>= 3.0.0). 87s linux-headers-6.8.0-11-generic depends on libssl3 (>= 3.0.0). 87s libsystemd-shared:arm64 depends on libssl3 (>= 3.0.0). 87s libssh-4:arm64 depends on libssl3 (>= 3.0.0). 87s libsasl2-modules:arm64 depends on libssl3 (>= 3.0.0). 87s libsasl2-2:arm64 depends on libssl3 (>= 3.0.0). 87s libpython3.12-minimal:arm64 depends on libssl3 (>= 3.0.0). 87s libnvme1 depends on libssl3 (>= 3.0.0). 87s libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). 87s libkmod2:arm64 depends on libssl3 (>= 3.0.0). 87s libfido2-1:arm64 depends on libssl3 (>= 3.0.0). 87s libcurl4:arm64 depends on libssl3 (>= 3.0.0). 87s libcryptsetup12:arm64 depends on libssl3 (>= 3.0.0). 87s kmod depends on libssl3 (>= 3.0.0). 87s dhcpcd-base depends on libssl3 (>= 3.0.0). 87s bind9-libs:arm64 depends on libssl3 (>= 3.0.0). 87s 87s (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 ... 74819 files and directories currently installed.) 87s Removing libssl3:arm64 (3.0.10-1ubuntu4) ... 87s Selecting previously unselected package libssl3t64:arm64. 87s (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 ... 74808 files and directories currently installed.) 87s Preparing to unpack .../libssl3t64_3.0.13-0ubuntu2_arm64.deb ... 87s Unpacking libssl3t64:arm64 (3.0.13-0ubuntu2) ... 88s Setting up libssl3t64:arm64 (3.0.13-0ubuntu2) ... 88s Setting up openssl (3.0.13-0ubuntu2) ... 88s Processing triggers for man-db (2.12.0-3) ... 88s Processing triggers for libc-bin (2.39-0ubuntu6) ... 90s Reading package lists... 90s Building dependency tree... 90s Reading state information... 90s 0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded. 91s sh: Attempting to set up Debian/Ubuntu apt sources automatically 91s sh: Distribution appears to be Ubuntu 92s Reading package lists... 93s Building dependency tree... 93s Reading state information... 93s eatmydata is already the newest version (131-1). 93s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s dbus is already the newest version (1.14.10-4ubuntu1). 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 95s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s rng-tools-debian is already the newest version (2.4). 97s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 97s Reading package lists... 97s Building dependency tree... 97s Reading state information... 97s The following packages will be REMOVED: 97s cloud-init* python3-configobj* python3-debconf* 98s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 98s After this operation, 3256 kB disk space will be freed. 98s (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 ... 74821 files and directories currently installed.) 98s Removing cloud-init (24.1.2-0ubuntu1) ... 99s Removing python3-configobj (5.0.8-3) ... 99s Removing python3-debconf (1.5.86) ... 99s Processing triggers for man-db (2.12.0-3) ... 99s (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 ... 74432 files and directories currently installed.) 99s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 100s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 100s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 100s invoke-rc.d: policy-rc.d denied execution of try-restart. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s linux-generic is already the newest version (6.8.0-11.11+1). 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 101s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 101s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 101s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 103s Reading package lists... 104s Reading package lists... 104s Building dependency tree... 104s Reading state information... 104s Calculating upgrade... 105s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 105s Reading package lists... 105s Building dependency tree... 105s Reading state information... 106s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 106s autopkgtest [18:02:06]: rebooting testbed after setup commands that affected boot 133s autopkgtest [18:02:33]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 02:53:31 UTC 2024 136s autopkgtest [18:02:36]: @@@@@@@@@@@@@@@@@@@@ apt-source stacks 138s Get:1 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (dsc) [2041 B] 138s Get:2 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (tar) [339 kB] 138s Get:3 http://ftpmaster.internal/ubuntu noble/universe stacks 2.66+dfsg-1 (diff) [12.1 kB] 139s gpgv: Signature made Tue Jan 23 12:37:41 2024 UTC 139s gpgv: using RSA key 4A31DB5A1EE4096C87399880903649294C33F9B7 139s gpgv: Can't check signature: No public key 139s dpkg-source: warning: cannot verify inline signature for ./stacks_2.66+dfsg-1.dsc: no acceptable signature found 139s autopkgtest [18:02:39]: testing package stacks version 2.66+dfsg-1 139s autopkgtest [18:02:39]: build not needed 140s autopkgtest [18:02:40]: test run-unit-test: preparing testbed 141s Reading package lists... 141s Building dependency tree... 141s Reading state information... 142s Starting pkgProblemResolver with broken count: 0 142s Starting 2 pkgProblemResolver with broken count: 0 142s Done 142s The following additional packages will be installed: 142s libdbi-perl libdeflate0 libgomp1 libhts3 libhtscodecs2 samtools stacks 142s Suggested packages: 142s libclone-perl libmldbm-perl libnet-daemon-perl libsql-statement-perl cwltool 142s gdb 142s Recommended packages: 142s libspreadsheet-writeexcel-perl littler 142s The following NEW packages will be installed: 142s autopkgtest-satdep libdbi-perl libdeflate0 libgomp1 libhts3 libhtscodecs2 142s samtools stacks 142s 0 upgraded, 8 newly installed, 0 to remove and 0 not upgraded. 142s Need to get 2978 kB/2978 kB of archives. 142s After this operation, 9199 kB of additional disk space will be used. 142s Get:1 /tmp/autopkgtest.wzpOyv/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [700 B] 142s Get:2 http://ftpmaster.internal/ubuntu noble/main arm64 libdbi-perl arm64 1.643-4build1 [718 kB] 143s Get:3 http://ftpmaster.internal/ubuntu noble/main arm64 libdeflate0 arm64 1.19-1 [43.4 kB] 143s Get:4 http://ftpmaster.internal/ubuntu noble/main arm64 libgomp1 arm64 14-20240303-1ubuntu1 [144 kB] 143s Get:5 http://ftpmaster.internal/ubuntu noble/universe arm64 libhtscodecs2 arm64 1.6.0-1 [78.1 kB] 143s Get:6 http://ftpmaster.internal/ubuntu noble/universe arm64 libhts3 arm64 1.18+ds-1 [422 kB] 143s Get:7 http://ftpmaster.internal/ubuntu noble/universe arm64 samtools arm64 1.19.2-1 [584 kB] 143s Get:8 http://ftpmaster.internal/ubuntu noble/universe arm64 stacks arm64 2.66+dfsg-1 [987 kB] 143s Fetched 2978 kB in 1s (3952 kB/s) 143s Selecting previously unselected package libdbi-perl:arm64. 143s (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 ... 74377 files and directories currently installed.) 143s Preparing to unpack .../0-libdbi-perl_1.643-4build1_arm64.deb ... 143s Unpacking libdbi-perl:arm64 (1.643-4build1) ... 143s Selecting previously unselected package libdeflate0:arm64. 143s Preparing to unpack .../1-libdeflate0_1.19-1_arm64.deb ... 143s Unpacking libdeflate0:arm64 (1.19-1) ... 143s Selecting previously unselected package libgomp1:arm64. 143s Preparing to unpack .../2-libgomp1_14-20240303-1ubuntu1_arm64.deb ... 143s Unpacking libgomp1:arm64 (14-20240303-1ubuntu1) ... 143s Selecting previously unselected package libhtscodecs2:arm64. 144s Preparing to unpack .../3-libhtscodecs2_1.6.0-1_arm64.deb ... 144s Unpacking libhtscodecs2:arm64 (1.6.0-1) ... 144s Selecting previously unselected package libhts3:arm64. 144s Preparing to unpack .../4-libhts3_1.18+ds-1_arm64.deb ... 144s Unpacking libhts3:arm64 (1.18+ds-1) ... 144s Selecting previously unselected package samtools. 144s Preparing to unpack .../5-samtools_1.19.2-1_arm64.deb ... 144s Unpacking samtools (1.19.2-1) ... 144s Selecting previously unselected package stacks. 144s Preparing to unpack .../6-stacks_2.66+dfsg-1_arm64.deb ... 144s Unpacking stacks (2.66+dfsg-1) ... 144s Selecting previously unselected package autopkgtest-satdep. 144s Preparing to unpack .../7-1-autopkgtest-satdep.deb ... 144s Unpacking autopkgtest-satdep (0) ... 144s Setting up libhtscodecs2:arm64 (1.6.0-1) ... 144s Setting up libdeflate0:arm64 (1.19-1) ... 144s Setting up libgomp1:arm64 (14-20240303-1ubuntu1) ... 144s Setting up libdbi-perl:arm64 (1.643-4build1) ... 144s Setting up libhts3:arm64 (1.18+ds-1) ... 144s Setting up samtools (1.19.2-1) ... 144s Setting up stacks (2.66+dfsg-1) ... 144s Setting up autopkgtest-satdep (0) ... 144s Processing triggers for man-db (2.12.0-3) ... 144s Processing triggers for libc-bin (2.39-0ubuntu6) ... 147s (Reading database ... 74692 files and directories currently installed.) 147s Removing autopkgtest-satdep (0) ... 148s autopkgtest [18:02:48]: test run-unit-test: [----------------------- 148s Stacks - a pipeline for building loci from short-read sequences 148s v2.66+dfsg http://creskolab.uoregon.edu/stacks/ 148s 148s This is the Stacks wrapper script for Debian. Usage: 148s stacks 148s 148s Programs available are: 148s clone_filter ref_map 148s cstacks sstacks 148s denovo_map stacks-dist-extract 148s gstacks stacks-gdb 148s kmer_filter stacks-integrate-alignments 148s phasedstacks stacks-samtools-tview 148s populations tsv2bam 148s process_radtags ustacks 148s process_shortreads 148s 148s Or else add /usr/libexec/stacks/bin to your $PATH to invoke the commands directly. 148s 148s clone_filter 2.66 148s 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] 148s f: path to the input file if processing single-end sequences. 148s p: path to a directory of files. 148s P: files contained within directory specified by '-p' are paired. 148s 1: first input file in a set of paired-end sequences. 148s 2: second input file in a set of paired-end sequences. 148s i: input file type, either 'bustard', 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default 'fastq'). 148s o: path to output the processed files. 148s y: output type, either 'fastq', 'fasta', 'gzfasta', or 'gzfastq' (default same as input type). 148s D: capture discarded reads to a file. 148s h: display this help message. 148s --oligo-len-1 len: length of the single-end oligo sequence in data set. 148s --oligo-len-2 len: length of the paired-end oligo sequence in data set. 148s --retain-oligo: do not trim off the random oligo sequence (if oligo is inline). 148s 148s Oligo sequence options: 148s --inline-null: random oligo is inline with sequence, occurs only on single-end read (default). 148s --null-inline: random oligo is inline with sequence, occurs only on the paired-end read. 148s --null-index: random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 148s --index-null: random oligo is provded in FASTQ header (Illumina i5 or i7 read). 148s --inline-inline: random oligo is inline with sequence, occurs on single and paired-end read. 148s --index-index: random oligo is provded in FASTQ header (Illumina i5 and i7 read). 148s --inline-index: random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header. 148s --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). 148s 148s cstacks 2.66 148s cstacks -P in_dir -M popmap [-n num_mismatches] [-p num_threads] 148s cstacks -s sample1_path [-s sample2_path ...] -o path [-n num_mismatches] [-p num_threads] 148s 148s -P,--in-path: path to the directory containing Stacks files. 148s -M,--popmap: path to a population map file. 148s -n: number of mismatches allowed between sample loci when build the catalog (default 1; suggested: set to ustacks -M). 148s -p,--threads: enable parallel execution with num_threads threads. 148s -s: sample prefix from which to load loci into the catalog. 148s -o,--outpath: output path to write results. 148s -c,--catalog : add to an existing catalog. 148s 148s Gapped assembly options: 148s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 148s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 148s --disable-gapped: disable gapped alignments between stacks (default: use gapped alignments). 148s 148s Advanced options: 148s --k-len : specify k-mer size for matching between between catalog loci (automatically calculated by default). 148s --report-mmatches: report query loci that match more than one catalog locus. 148s denovo_map.pl 2.66 148s denovo_map.pl --samples dir --popmap path --out-path dir [--paired [--rm-pcr-duplicates]] (assembly options) (filtering options) [-X prog:"opts" ...] 148s 148s Input/Output files: 148s --samples: path to the directory containing the reads files for each sample. 148s --popmap: path to a population map file (format is " TAB ", one sample per line). 148s -o,--out-path: path to an output directory. 148s 148s General options: 148s -X: additional options for specific pipeline components, e.g. -X "populations: --min-maf 0.05". 148s -T, --threads: the number of threads/CPUs to use (default: 1). 148s --dry-run: dry run. Do not actually execute anything, just print the commands that would be executed. 148s --resume: resume executing the pipeline from a previous run. 148s 148s Stack assembly options: 148s -M: number of mismatches allowed between stacks within individuals (for ustacks). 148s -n: number of mismatches allowed between stacks between individuals (for cstacks; default: set to ustacks -M). 148s 148s SNP model options: 148s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 148s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 148s 148s Paired-end options: 148s --paired: after assembling RAD loci, assemble mini-contigs with paired-end reads. 148s --rm-pcr-duplicates: remove all but one set of read pairs of the same sample that have 148s the same insert length. 148s 148s Population filtering options: 148s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 148s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 148s 148s For large datasets: 148s --catalog-popmap: path to a second population map file containing a subset of samples for use only in building the catalog. 148s 148s Miscellaneous: 148s --time-components (for benchmarking) 148s gstacks 2.66 148s 148s De novo mode: 148s gstacks -P stacks_dir -M popmap 148s 148s -P: input directory containing '*.matches.bam' files created by the 148s de novo Stacks pipeline, ustacks-cstacks-sstacks-tsv2bam 148s 148s Reference-based mode: 148s gstacks -I bam_dir -M popmap [-S suffix] -O out_dir 148s gstacks -B bam_file [-B ...] -O out_dir 148s 148s -I: input directory containing BAM files 148s -S: with -I/-M, suffix to use to build BAM file names: by default this 148s is just '.bam', i.e. the program expects 'SAMPLE_NAME.bam' 148s -B: input BAM file(s) 148s 148s The input BAM file(s) must be sorted by coordinate. 148s With -B, records must be assigned to samples using BAM "reads groups" 148s (gstacks uses the ID/identifier and SM/sample name fields). Read groups 148s must be consistent if repeated different files. Note that with -I, read 148s groups are unneeded and ignored. 148s 148s For both modes: 148s -M: path to a population map giving the list of samples 148s -O: output directory (default: none with -B; with -P same as the input 148s directory) 148s -t,--threads: number of threads to use (default: 1) 148s 148s SNP Model options: 148s --model: model to use to call variants and genotypes; one of 148s marukilow (default), marukihigh, or snp 148s --var-alpha: alpha threshold for discovering SNPs (default: 0.01 for marukilow) 148s --gt-alpha: alpha threshold for calling genotypes (default: 0.05) 148s 148s Paired-end options: 148s --rm-pcr-duplicates: remove all but one set ofread pairs of the same sample that 148s have the same insert length (implies --rm-unpaired-reads) 148s --rm-unpaired-reads: discard unpaired reads 148s --ignore-pe-reads: ignore paired-end reads even if present in the input 148s --unpaired: ignore read pairing (only for paired-end GBS; treat READ2's as if they were READ1's) 148s 148s Advanced options: 148s (De novo mode) 148s --kmer-length: kmer length for the de Bruijn graph (default: 31, max. 31) 148s --max-debruijn-reads: maximum number of reads to use in the de Bruijn graph (default: 1000) 148s --min-kmer-cov: minimum coverage to consider a kmer (default: 2) 148s --write-alignments: save read alignments (heavy BAM files) 148s 148s (Reference-based mode) 148s --methyl-status: assumes a methylation-aware molecular protocol used; calls methylated bases. 148s --min-mapq: minimum PHRED-scaled mapping quality to consider a read (default: 10) 148s --max-clipped: maximum soft-clipping level, in fraction of read length (default: 0.20) 148s --max-insert-len: maximum allowed sequencing insert length (default: 1000) 148s 148s --details: write a heavier output 148s --phasing-cooccurrences-thr-range: range of edge coverage thresholds to 148s iterate over when building the graph of allele cooccurrences for 148s SNP phasing (default: 1,2) 148s --phasing-dont-prune-hets: don't try to ignore dubious heterozygote 148s genotypes during phasing 148s 148s kmer_filter 2.66 148s 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] 148s f: path to the input file if processing single-end seqeunces. 148s i: input file type, either 'bustard' for the Illumina BUSTARD output files, 'fasta', 'fastq', 'gzfasta', or 'gzfastq' (default 'fastq'). 148s p: path to a directory of files (for single-end files only). 148s 1: specify the first in a pair of files to be processed together. 148s 2: specify the second in a pair of files to be processed together. 148s o: path to output the processed files. 148s y: output type, either 'fastq' or 'fasta' (default fastq). 148s D: capture discarded reads to a file. 148s h: display this help message. 148s 148s Filtering options: 148s --rare: turn on filtering based on rare k-mers. 148s --abundant: turn on filtering based on abundant k-mers. 148s --k-len : specify k-mer size (default 15). 148s 148s Advanced filtering options: 148s --max-k-freq : specify the number of times a kmer must occur to be considered abundant (default 20,000). 148s --min-lim : specify number of rare kmers occurring in a row required to discard a read (default 80% of the k-mer length). 148s --max-lim : specify number of abundant kmers required to discard a read (default 80% of the k-mers in a read). 148s 148s Normalize data: 148s --normalize : normalize read depth according to k-mer coverage. 148s 148s Characterizing K-mers: 148s --write-k-freq: write kmers along with their frequency of occurrence and exit. 148s --k-dist: print k-mer frequency distribution and exit. 148s 148s Advanced input options: 148s --read-k-freq : read a set of kmers along with their frequencies of occurrence instead of reading raw input files. 148s 148s phasedstacks 2.66 148s phasedstacks -b id -S path -P path -t file_type [-p threads] [-M popmap] [-v] [-h] 148s b: Stacks batch ID. 148s P: path to the phased output files. 148s S: path to the Stacks output files. 148s t: input file type. Supported types: fastphase, and beagle. 148s p: number of processes to run in parallel sections of code. 148s M: path to the population map, a tab separated file describing which individuals belong in which population. 148s v: print program version. 148s h: display this help message. 148s --haplotypes: data were phased as RAD locus haplotypes. 148s --dprime-bin-size: size of buckets for binning SNPs at a particular distance to calculate the mean D' value. 148s --dprime-threshold : if D' values fall above , set the D' to 1, otherwise set D' to 0. 148s 148s Filtering options: 148s --skip-zeros: do not include D' values of zero in the D' output. 148s --minor-allele-freq: specify a minimum minor allele frequency required to process a nucleotide site (0 < a < 0.5). 148s --min-inform-pairs: when building D' haplotype blocks, the minimum number of informative D' measures to combine two blocks (default 0.9). 148s 148s populations 2.66 148s Usage: 148s populations -P dir [-O dir] [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 148s populations -V vcf -O dir [-M popmap] (filters) [--fstats] [-k [--sigma=150000] [--bootstrap [-N 100]]] (output formats) 148s 148s -P,--in-path: path to a directory containing Stacks output files. 148s -V,--in-vcf: path to a standalone input VCF file. 148s -O,--out-path: path to a directory where to write the output files. (Required by -V; otherwise defaults to value of -P.) 148s -M,--popmap: path to a population map. (Format is 'SAMPLE1 \t POP1 \n SAMPLE2 ...'.) 148s -t,--threads: number of threads to run in parallel sections of code. 148s --batch-size [int]: the number of loci to process in a batch (default: 10,000 in de novo mode; in reference mode, one chromosome 148s per batch). Increase to speed analysis, uses more memory, decrease to save memory). 148s 148s Data Filtering: 148s -p,--min-populations [int]: minimum number of populations a locus must be present in to process a locus. 148s -r,--min-samples-per-pop [float]: minimum percentage of individuals in a population required to process a locus for that population. 148s -R,--min-samples-overall [float]: minimum percentage of individuals across populations required to process a locus. 148s -H,--filter-haplotype-wise: apply the above filters haplotype wise 148s (unshared SNPs will be pruned to reduce haplotype-wise missing data). 148s --min-maf [float]: specify a minimum minor allele frequency required to process a SNP (0 < min_maf < 0.5; applied to the metapopulation). 148s --min-mac [int]: specify a minimum minor allele count required to process a SNP (applied to the metapopulation). 148s --max-obs-het [float]: specify a maximum observed heterozygosity required to process a SNP (applied ot the metapopulation). 148s 148s --write-single-snp: restrict data analysis to only the first SNP per locus (implies --no-haps). 148s --write-random-snp: restrict data analysis to one random SNP per locus (implies --no-haps). 148s -B,--blacklist: path to a file containing Blacklisted markers to be excluded from the export. 148s -W,--whitelist: path to a file containing Whitelisted markers to include in the export. 148s 148s Locus stats: 148s --hwe: calculate divergence from Hardy-Weinberg equilibrium for each locus. 148s 148s Fstats: 148s --fstats: enable SNP and haplotype-based F statistics. 148s --fst-correction: specify a p-value correction to be applied to Fst values based on a Fisher's exact test. Default: off. 148s --p-value-cutoff [float]: maximum p-value to keep an Fst measurement. Default: 0.05. 148s 148s Kernel-smoothing algorithm: 148s -k,--smooth: enable kernel-smoothed Pi, Fis, Fst, Fst', and Phi_st calculations. 148s --smooth-fstats: enable kernel-smoothed Fst, Fst', and Phi_st calculations. 148s --smooth-popstats: enable kernel-smoothed Pi and Fis calculations. 148s (Note: turning on smoothing implies --ordered-export.) 148s --sigma [int]: standard deviation of the kernel smoothing weight distribution. Sliding window size is defined as 3 x sigma; (default sigma = 150kbp). 148s --bootstrap-archive: archive statistical values for use in bootstrap resampling in a subsequent run, statistics must be enabled to be archived. 148s --bootstrap: turn on boostrap resampling for all kernel-smoothed statistics. 148s -N,--bootstrap-reps [int]: number of bootstrap resamplings to calculate (default 100). 148s --bootstrap-pifis: turn on boostrap resampling for smoothed SNP-based Pi and Fis calculations. 148s --bootstrap-fst: turn on boostrap resampling for smoothed Fst calculations based on pairwise population comparison of SNPs. 148s --bootstrap-div: turn on boostrap resampling for smoothed haplotype diveristy and gene diversity calculations based on haplotypes. 148s --bootstrap-phist: turn on boostrap resampling for smoothed Phi_st calculations based on haplotypes. 148s --bootstrap-wl [path]: only bootstrap loci contained in this whitelist. 148s 148s File output options: 148s --ordered-export: if data is reference aligned, exports will be ordered; only a single representative of each overlapping site. 148s --fasta-loci: output locus consensus sequences in FASTA format. 148s --fasta-samples: output the sequences of the two haplotypes of each (diploid) sample, for each locus, in FASTA format. 148s --vcf: output SNPs and haplotypes in Variant Call Format (VCF). 148s --vcf-all: output all sites in Variant Call Format (VCF). 148s --genepop: output SNPs and haplotypes in GenePop format. 148s --structure: output results in Structure format. 148s --radpainter: output results in fineRADstructure/RADpainter format. 148s --plink: output genotypes in PLINK format. 148s --hzar: output genotypes in Hybrid Zone Analysis using R (HZAR) format. 148s --phylip: output nucleotides that are fixed-within, and variant among populations in Phylip format for phylogenetic tree construction. 148s --phylip-var: include variable sites in the phylip output encoded using IUPAC notation. 148s --phylip-var-all: include all sequence as well as variable sites in the phylip output encoded using IUPAC notation. 148s --treemix: output SNPs in a format useable for the TreeMix program (Pickrell and Pritchard). 148s --gtf: output locus positions in a GTF annotation file. 148s --no-hap-exports: omit haplotype outputs. 148s --fasta-samples-raw: output all haplotypes observed in each sample, for each locus, in FASTA format. 148s 148s Genetic map output options (population map must specify a genetic cross): 148s --map-type: genetic map type to write. 'CP', 'DH', 'F2', and 'BC1' are the currently supported map types. 148s --map-format: mapping program format to write, 'joinmap', 'onemap', and 'rqtl' are currently supported. 148s 148s Additional options: 148s -h,--help: display this help message. 148s -v,--version: print program version. 148s --verbose: turn on additional logging. 148s --log-fst-comp: log components of Fst/Phi_st calculations to a file. 148s process_radtags 2.66 148s process_radtags -p in_dir [-P] [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 148s process_radtags -f in_file [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 148s 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] 148s process_radtags -1 pair_1 -2 pair_2 [-b barcode_file] -o out_dir -e enz [--threads num] [-c] [-q] [-r] [-t len] 148s 148s -p,--in-path: path to a directory of files. 148s -P,--paired: files contained within the directory are paired. 148s -I,--interleaved: specify that the paired-end reads are interleaved in single files. 148s -i,--in-type: input file type, either 'fastq', 'gzfastq' (gzipped fastq), 'bam', or 'bustard' (default: guess, or gzfastq if unable to). 148s -b,--barcodes: path to a file containing barcodes for this run, omit to ignore any barcoding or for already demultiplexed data. 148s -o,--out-path: path to output the processed files. 148s -f: path to the input file if processing single-end sequences. 148s -1: first input file in a set of paired-end sequences. 148s -2: second input file in a set of paired-end sequences. 148s --threads: number of threads to run. 148s -c,--clean: clean data, remove any read with an uncalled base ('N'). 148s -q,--quality: discard reads with low quality (phred) scores. 148s -r,--rescue: rescue barcodes and RAD-Tag cut sites. 148s -t,--truncate: truncate final read length to this value. 148s -D,--discards: capture discarded reads to a file. 148s -y,--out-type: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default: match input type). 148s 148s Barcode options: 148s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 148s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 148s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 148s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 148s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 148s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 148s --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). 148s 148s Restriction enzyme options: 148s -e [enz], --renz-1 [enz]: provide the restriction enzyme used (cut site occurs on single-end read) 148s --renz-2 [enz]: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). 148s Currently supported enzymes include: 148s 'aciI', 'aclI', 'ageI', 'aluI', 'apaLI', 'apeKI', 'apoI', 'aseI', 148s 'bamHI', 'bbvCI', 'bfaI', 'bfuCI', 'bgIII', 'bsaHI', 'bspDI', 'bstYI', 148s 'btgI', 'cac8I', 'claI', 'csp6I', 'ddeI', 'dpnII', 'eaeI', 'ecoRI', 148s 'ecoRV', 'ecoT22I', 'haeII', 'haeIII', 'hhaI', 'hinP1I', 'hindIII', 'hpaII', 148s 'hpyCH4IV', 'kpnI', 'mluCI', 'mseI', 'mslI', 'mspI', 'ncoI', 'ndeI', 148s 'ngoMIV', 'nheI', 'nlaIII', 'notI', 'nsiI', 'nspI', 'pacI', 'pspXI', 148s 'pstI', 'pstIshi', 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 148s 'speI', 'sphI', 'taqI', 'xbaI', or 'xhoI' 148s 148s Protocol-specific options: 148s --bestrad: library was generated using BestRAD, check for restriction enzyme on either read and potentially tranpose reads. 148s --methylrad: library was generated using enzymatic methyl-seq (EM-seq) or bisulphite sequencing. 148s 148s Adapter options: 148s --adapter-1 : provide adaptor sequence that may occur on the single-end read for filtering. 148s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 148s --adapter-mm : number of mismatches allowed in the adapter sequence. 148s 148s Output options: 148s --retain-header: retain unmodified FASTQ headers in the output. 148s --merge: if no barcodes are specified, merge all input files into a single output file. 148s 148s Advanced options: 148s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 148s --disable-rad-check: disable checking if the RAD cut site is intact. 148s --encoding: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 148s --window-size: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 148s --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). 148s --len-limit : specify a minimum sequence length (useful if your data has already been trimmed). 148s --barcode-dist-1: the number of allowed mismatches when rescuing single-end barcodes (default 1). 148s --barcode-dist-2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode-dist-1). 148s process_shortreads 2.66 148s 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] 148s f: path to the input file if processing single-end seqeunces. 148s i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. 148s p: path to a directory of single-end Illumina files. 148s 1: first input file in a set of paired-end sequences. 148s 2: second input file in a set of paired-end sequences. 148s P: specify that input is paired (for use with '-p'). 148s I: specify that the paired-end reads are interleaved in single files. 148s o: path to output the processed files. 148s y: output type, either 'fastq' or 'fasta' (default gzfastq). 148s b: a list of barcodes for this run. 148s c: clean data, remove any read with an uncalled base. 148s q: discard reads with low quality scores. 148s r: rescue barcodes. 148s t: truncate final read length to this value. 148s E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+/Sanger, default) or 'phred64' (Illumina 1.3-1.5). 148s D: capture discarded reads to a file. 148s w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). 148s s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). 148s h: display this help message. 148s 148s Barcode options: 148s --inline-null: barcode is inline with sequence, occurs only on single-end read (default). 148s --index-null: barcode is provded in FASTQ header (Illumina i5 or i7 read). 148s --null-index: barcode is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided). 148s --inline-inline: barcode is inline with sequence, occurs on single and paired-end read. 148s --index-index: barcode is provded in FASTQ header (Illumina i5 and i7 reads). 148s --inline-index: barcode is inline with sequence on single-end read and occurs in FASTQ header (from either i5 or i7 read). 148s --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). 148s 148s Adapter options: 148s --adapter-1 : provide adaptor sequence that may occur on the first read for filtering. 148s --adapter-2 : provide adaptor sequence that may occur on the paired-read for filtering. 148s --adapter-mm : number of mismatches allowed in the adapter sequence. 148s 148s Output options: 148s --retain-header: retain unmodified FASTQ headers in the output. 148s --merge: if no barcodes are specified, merge all input files into a single output file (or single pair of files). 148s 148s Advanced options: 148s --no-read-trimming: do not trim low quality reads, just discard them. 148s --len-limit : when trimming sequences, specify the minimum length a sequence must be to keep it (default 31bp). 148s --filter-illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. 148s --barcode-dist: provide the distace between barcodes to allow for barcode rescue (default 2) 148s --mate-pair: raw reads are circularized mate-pair data, first read will be reverse complemented. 148s --no-overhang: data does not contain an overhang nucleotide between barcode and seqeunce. 148s ref_map.pl 2.66 148s ref_map.pl --samples path --popmap path [-s spacer] --out-path path [--rm-pcr-duplicates] [-X prog:"opts" ...] 148s 148s Input/Output files: 148s --samples: path to the directory containing the samples BAM (or SAM) alignment files. 148s --popmap: path to a population map file (format is " TAB ", one sample per line). 148s -s: spacer for file names: by default this is empty and the program looks for files 148s named 'SAMPLE_NAME.bam'; if this option is given the program looks for files 148s named 'SAMPLE_NAME.SPACER.bam'. 148s -o,--out-path: path to an output directory. 148s 148s General options: 148s -X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50" 148s -T: the number of threads/CPUs to use (default: 1). 148s -d: Dry run. Do not actually execute anything, just print the individual pipeline commands 148s that would be executed. 148s 148s SNP model options: 148s --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05). 148s --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05). 148s 148s Paired-end options: 148s --rm-pcr-duplicates: remove all but one copy of read pairs of the same sample that have 148s the same insert length. 148s --ignore-pe-reads: ignore paired-end reads even if present in the input 148s --unpaired: ignore read pairing (for paired-end GBS; treat READ2's as if they were READ1's) 148s 148s Population filtering options: 148s -r,--min-samples-per-pop: minimum percentage of individuals in a population required to process a locus for that population (for populations; default: 0) 148s -p,--min-populations: minimum number of populations a locus must be present in to process a locus (for populations; default: 1) 148s 148s Miscellaneous: 148s --time-components (for benchmarking) 148s sstacks 2.66 148s sstacks -P dir -M popmap [-p n_threads] 148s sstacks -c catalog_path -s sample_path [-s sample_path ...] -o path [-p n_threads] 148s -P,--in-path: path to the directory containing Stacks files. 148s -M,--popmap: path to a population map file from which to take sample names. 148s -s,--sample: filename prefix from which to load sample loci. 148s -c,--catalog: path to the catalog. 148s -p,--threads: enable parallel execution with n_threads threads. 148s -o,--out-path: output path to write results. 148s -x: don't verify haplotype of matching locus. 148s 148s Gapped assembly options: 148s --disable-gapped: disable gapped alignments between stacks (default: enable gapped alignments). 148s usage: 148s stacks-dist-extract logfile [section] 148s stacks-dist-extract [--pretty] [--out-path path] logfile [section] 148s cat logfile | stacks-dist-extract [--pretty] [--section section] 148s 148s Export a paricular section of a Stacks log or distribs file. If you supply a 148s log path alone, stacks-dist-extract will print the available sections to 148s output. The log file can also be supplied via stdin. 148s 148s options: 148s -h, --help show this help message and exit 148s -p, --pretty Output data as a table with columns lined up. 148s -o path, --out-path path 148s Path to output file. 148s -s section, --section section 148s Name of section to output from the log file. 148s Usage: 148s stacks-gdb PROGRAM ARGUMENTS 148s 148s e.g. 148s stacks-gdb populations -P . -p 3 -r 0.5 --vcf 148s 148s This utility will run the `PROGRAM ARGUMENTS` command as specified, but in 148s case of a crash it will print additional information, helping us in fixing the 148s crash. 148s 148s This utility requires GDB, the GNU Debugger, to be installed on the system where 148s Stacks is run. You can check whether this is the case by just typing: 148s 148s gdb --version 148s 148s at the command prompt. Note that you may need to load the corresponding module. 148s GDB is standard scientific software, but may not be installed on some systems. 148s For further information please contact the administrators of your system; 148s trying to install GDB without administrator priviledges is not recommended. 148s 148s For questions please contact us, e.g. at stacks-users@googlegroups.com 148s usage: stacks-integrate-alignments [-h] -P path -B path -O path [-q MIN_MAPQ] 148s [-a MIN_ALNCOV] [-p MIN_PCTID] [--verbose] 148s [--version] 148s 148s Extracts the coordinates of the RAD loci from the given BAM file into a 148s 'locus_coordinates.tsv' table, then rewrites the 'catalog.fa.gz' and 148s 'catalog.calls' files so that they include the genomic coordinates given in 148s the input BAM file. 148s 148s options: 148s -h, --help show this help message and exit 148s -P path, --in-path path 148s Path to a directory containing Stacks ouput files. 148s -B path, --bam-path path 148s Path to a SAM or BAM file containing alignment of de 148s novo catalog loci to a reference genome. 148s -O path, --out-path path 148s Path to write the integrated ouput files. 148s -q MIN_MAPQ, --min_mapq MIN_MAPQ 148s Minimum mapping quality as listed in the BAM file 148s (default 20). 148s -a MIN_ALNCOV, --min_alncov MIN_ALNCOV 148s Minimum fraction of the de novo catalog locus that 148s must participate in the alignment (default 0.6). 148s -p MIN_PCTID, --min_pctid MIN_PCTID 148s Minimum BLAST-style percent identity of the largest 148s alignment fragment for a de novo catalog locus 148s (default 0.6). 148s --verbose Provide verbose output. 148s --version show program's version number and exit 148s usage: 148s stacks-samtools-tview -P gstacks_dir -c catalog_locus_id -s sample_name 148s 148s Displays the read alignments of the given sample for the given locus, in text 148s format, to the standard output. Requires gstacks to have been run with the 148s --write-alignments option. (This is a convenience wrapper around samtools-tview.) 148s tsv2bam 2.66 148s tsv2bam -P stacks_dir -M popmap [-R paired_reads_dir] 148s tsv2bam -P stacks_dir -s sample [-s sample ...] [-R paired_reads_dir] 148s 148s -P,--in-dir: input directory. 148s -M,--popmap: population map. 148s -s,--sample: name of one sample. 148s -R,--pe-reads-dir: directory where to find the paired-end reads files (in fastq/fasta/bam (gz) format). 148s -t: number of threads to use (default: 1). 148s 148s ustacks 2.66 148s ustacks -f file_path -o path [-M max_dist] [-m min_cov] [-p num_threads] 148s f: input file path. 148s o: output path to write results. 148s M: Maximum distance (in nucleotides) allowed between stacks (default 2). 148s m: Minimum depth of coverage required to create a stack (default 3). 148s N: Maximum distance allowed to align secondary reads to primary stacks (default: M + 2). 148s p: enable parallel execution with num_threads threads. 148s t: input file type. Supported types: fasta, fastq, gzfasta, or gzfastq (default: guess). 148s --name: a name for the sample (default: input file name minus the suffix). 148s R: retain unused reads. 148s H: disable calling haplotypes from secondary reads. 148s 148s Stack assembly options: 148s --force-diff-len: allow raw input reads of different lengths, e.g. after trimming (default: ustacks prefers raw input reads of uniform length). 148s --keep-high-cov: disable the algorithm that removes highly-repetitive stacks and nearby errors. 148s --high-cov-thres: highly-repetitive stacks threshold, in standard deviation units (default: 3.0). 148s --max-locus-stacks : maximum number of stacks at a single de novo locus (default 3). 148s --k-len : specify k-mer size for matching between alleles and loci (automatically calculated by default). 148s --deleverage: enable the Deleveraging algorithm, used for resolving over merged tags. 148s 148s Gapped assembly options: 148s --max-gaps: number of gaps allowed between stacks before merging (default: 2). 148s --min-aln-len: minimum length of aligned sequence in a gapped alignment (default: 0.80). 148s 148s --disable-gapped: do not preform gapped alignments between stacks (default: gapped alignements enabled). 148s Model options: 148s --model-type: either 'snp' (default), 'bounded', or 'fixed' 148s For the SNP or Bounded SNP model: 148s --alpha : chi square significance level required to call a heterozygote or homozygote, either 0.1, 0.05 (default), 0.01, or 0.001. 148s For the Bounded SNP model: 148s --bound-low : lower bound for epsilon, the error rate, between 0 and 1.0 (default 0). 148s --bound-high : upper bound for epsilon, the error rate, between 0 and 1.0 (default 1). 148s For the Fixed model: 148s --bc-err-freq : specify the barcode error frequency, between 0 and 1.0. 148s 148s h: display this help message. 148s autopkgtest [18:02:48]: test run-unit-test: -----------------------] 149s autopkgtest [18:02:49]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 149s run-unit-test PASS (superficial) 150s autopkgtest [18:02:50]: @@@@@@@@@@@@@@@@@@@@ summary 150s run-unit-test PASS (superficial) 154s Creating nova instance adt-noble-arm64-stacks-20240324-174632-juju-7f2275-prod-proposed-migration-environment-3 from image adt/ubuntu-noble-arm64-server-20240324.img (UUID 943dd583-2042-4622-b4ce-bdf10ad153ac)...