Diff of the two buildlogs: -- --- b1/build.log 2025-02-22 00:15:12.672271718 +0000 +++ b2/build.log 2025-02-22 00:16:49.187883008 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Mar 26 18:33:54 -12 2026 -I: pbuilder-time-stamp: 1774593234 +I: Current time: Sat Feb 22 14:15:15 +14 2025 +I: pbuilder-time-stamp: 1740183315 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -27,52 +27,84 @@ dpkg-source: info: applying make-4.4.1.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1272158/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/671649/tmp/hooks/D01_modify_environment starting +debug: Running on codethink04-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 22 00:15 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/671649/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/671649/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='arm64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='308a4e9ee74c445286fdee80d0e2ecf2' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='1272158' - PS1='# ' - PS2='> ' + INVOCATION_ID=12b53ee092914f6c9077280e15654abf + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=671649 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.pzeb5dlB/pbuilderrc_owMa --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pzeb5dlB/b1 --logfile b1/build.log snippy_4.6.0+dfsg-5.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.pzeb5dlB/pbuilderrc_03bD --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pzeb5dlB/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1272158/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/671649/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -554,7 +586,7 @@ Get: 414 http://deb.debian.org/debian trixie/main arm64 snp-sites arm64 2.5.1-2+b2 [14.0 kB] Get: 415 http://deb.debian.org/debian trixie/main arm64 snpeff all 5.2.f+dfsg-1 [7244 B] Get: 416 http://deb.debian.org/debian trixie/main arm64 vt arm64 0.57721+ds-3+b2 [720 kB] -Fetched 314 MB in 4s (88.4 MB/s) +Fetched 314 MB in 1s (253 MB/s) Preconfiguring packages ... Selecting previously unselected package libsystemd-shared:arm64. (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 ... 19923 files and directories currently installed.) @@ -1922,8 +1954,8 @@ Setting up tzdata (2025a-2) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Mar 27 06:36:16 UTC 2026. -Universal Time is now: Fri Mar 27 06:36:16 UTC 2026. +Local time is now: Sat Feb 22 00:16:06 UTC 2025. +Universal Time is now: Sat Feb 22 00:16:06 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -2450,7 +2482,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../snippy_4.6.0+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/671649/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/671649/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../snippy_4.6.0+dfsg-5_source.changes dpkg-buildpackage: info: source package snippy dpkg-buildpackage: info: source version 4.6.0+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -2476,54 +2512,54 @@ [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq -[18:37:21] This is snippy 4.6.0 -[18:37:21] Written by Torsten Seemann -[18:37:21] Obtained from https://github.com/tseemann/snippy -[18:37:21] Detected operating system: linux -[18:37:21] Enabling bundled linux tools. -[18:37:21] Found bwa - /usr/bin/bwa -[18:37:21] Found bcftools - /usr/bin/bcftools -[18:37:21] Found samtools - /usr/bin/samtools -[18:37:21] Found java - /usr/bin/java -[18:37:21] Found snpEff - /usr/bin/snpEff -[18:37:21] Found samclip - /usr/bin/samclip -[18:37:21] Found seqtk - /usr/bin/seqtk -[18:37:21] Found parallel - /usr/bin/parallel -[18:37:21] Found freebayes - /usr/bin/freebayes -[18:37:21] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[18:37:21] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[18:37:21] Found vcfstreamsort - /usr/bin/vcfstreamsort -[18:37:21] Found vcfuniq - /usr/bin/vcfuniq -[18:37:21] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[18:37:21] Found gzip - /usr/bin/gzip -[18:37:21] Found vt - /usr/bin/vt -[18:37:21] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[18:37:22] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[18:37:22] Checking version: samtools --version is >= 1.7 - ok, have 1.21 -[18:37:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 -[18:37:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[18:37:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[18:37:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[18:37:22] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[18:37:22] Treating reference as 'fasta' format. -[18:37:22] Will use 2 CPU cores. -[18:37:22] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq -[18:37:22] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[18:37:22] Used --force, will overwrite existing S1 -[18:37:22] Changing working directory: S1 -[18:37:22] Creating reference folder: reference -[18:37:22] Extracting FASTA and GFF from reference. -[18:37:22] Wrote 3 sequences to ref.fa -[18:37:22] Wrote 0 features to ref.gff -[18:37:22] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[18:37:22] Using BAM RG (Read Group) ID: S1 -[18:37:22] Running: samtools faidx reference/ref.fa 2>> snps.log -[18:37:22] Running: bwa index reference/ref.fa 2>> snps.log -[18:37:23] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[18:37:23] Running: ln -sf reference/ref.fa . 2>> snps.log -[18:37:23] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[18:37:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[18:37:23] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[14:16:25] This is snippy 4.6.0 +[14:16:25] Written by Torsten Seemann +[14:16:25] Obtained from https://github.com/tseemann/snippy +[14:16:25] Detected operating system: linux +[14:16:25] Enabling bundled linux tools. +[14:16:25] Found bwa - /usr/bin/bwa +[14:16:25] Found bcftools - /usr/bin/bcftools +[14:16:25] Found samtools - /usr/bin/samtools +[14:16:25] Found java - /usr/bin/java +[14:16:25] Found snpEff - /usr/bin/snpEff +[14:16:25] Found samclip - /usr/bin/samclip +[14:16:25] Found seqtk - /usr/bin/seqtk +[14:16:25] Found parallel - /usr/bin/parallel +[14:16:25] Found freebayes - /usr/bin/freebayes +[14:16:25] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[14:16:25] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[14:16:25] Found vcfstreamsort - /usr/bin/vcfstreamsort +[14:16:25] Found vcfuniq - /usr/bin/vcfuniq +[14:16:25] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[14:16:25] Found gzip - /usr/bin/gzip +[14:16:25] Found vt - /usr/bin/vt +[14:16:25] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[14:16:25] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[14:16:25] Checking version: samtools --version is >= 1.7 - ok, have 1.21 +[14:16:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 +[14:16:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[14:16:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[14:16:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[14:16:25] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[14:16:25] Treating reference as 'fasta' format. +[14:16:25] Will use 2 CPU cores. +[14:16:25] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq +[14:16:25] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq +[14:16:25] Used --force, will overwrite existing S1 +[14:16:25] Changing working directory: S1 +[14:16:25] Creating reference folder: reference +[14:16:25] Extracting FASTA and GFF from reference. +[14:16:25] Wrote 3 sequences to ref.fa +[14:16:25] Wrote 0 features to ref.gff +[14:16:25] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[14:16:25] Using BAM RG (Read Group) ID: S1 +[14:16:25] Running: samtools faidx reference/ref.fa 2>> snps.log +[14:16:25] Running: bwa index reference/ref.fa 2>> snps.log +[14:16:26] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[14:16:26] Running: ln -sf reference/ref.fa . 2>> snps.log +[14:16:26] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[14:16:26] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[14:16:26] Running: bwa mem -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) @@ -2538,17 +2574,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 437) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 1.309 CPU sec, 2.555 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.373 CPU sec, 0.689 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[main] Real time: 2.840 sec; CPU: 1.336 sec +[main] Real time: 0.845 sec; CPU: 1.442 sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. -[18:37:27] Running: samtools index snps.bam 2>> snps.log -[18:37:27] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[18:37:27] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[18:37:30] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[14:16:27] Running: samtools index snps.bam 2>> snps.log +[14:16:27] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[14:16:27] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[14:16:28] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -2585,43 +2621,43 @@ Time elapsed: 0.01s -[18:37:30] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[18:37:30] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[18:37:31] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[18:37:31] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[18:37:31] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[18:37:31] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[18:37:31] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[18:37:31] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[18:37:31] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[18:37:31] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[18:37:31] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[18:37:32] Marked 749 heterozygous sites with 'n' -[18:37:32] Creating extra output files: BED GFF CSV TXT HTML -[18:37:32] Identified 261 variants. -[18:37:32] Result folder: S1 -[18:37:32] Result files: -[18:37:32] * S1/snps.aligned.fa -[18:37:32] * S1/snps.bam -[18:37:32] * S1/snps.bam.bai -[18:37:32] * S1/snps.bed -[18:37:32] * S1/snps.consensus.fa -[18:37:32] * S1/snps.consensus.subs.fa -[18:37:32] * S1/snps.csv -[18:37:32] * S1/snps.filt.vcf -[18:37:32] * S1/snps.gff -[18:37:32] * S1/snps.html -[18:37:32] * S1/snps.log -[18:37:32] * S1/snps.raw.vcf -[18:37:32] * S1/snps.subs.vcf -[18:37:32] * S1/snps.tab -[18:37:32] * S1/snps.txt -[18:37:32] * S1/snps.vcf -[18:37:32] * S1/snps.vcf.gz -[18:37:32] * S1/snps.vcf.gz.csi -[18:37:32] Walltime used: 11 seconds -[18:37:32] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues -[18:37:32] Done. +[14:16:28] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[14:16:28] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[14:16:29] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[14:16:29] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[14:16:29] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[14:16:29] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[14:16:29] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[14:16:29] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[14:16:29] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[14:16:29] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[14:16:29] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[14:16:29] Marked 749 heterozygous sites with 'n' +[14:16:29] Creating extra output files: BED GFF CSV TXT HTML +[14:16:29] Identified 261 variants. +[14:16:29] Result folder: S1 +[14:16:29] Result files: +[14:16:29] * S1/snps.aligned.fa +[14:16:29] * S1/snps.bam +[14:16:29] * S1/snps.bam.bai +[14:16:29] * S1/snps.bed +[14:16:29] * S1/snps.consensus.fa +[14:16:29] * S1/snps.consensus.subs.fa +[14:16:29] * S1/snps.csv +[14:16:29] * S1/snps.filt.vcf +[14:16:29] * S1/snps.gff +[14:16:29] * S1/snps.html +[14:16:29] * S1/snps.log +[14:16:29] * S1/snps.raw.vcf +[14:16:29] * S1/snps.subs.vcf +[14:16:29] * S1/snps.tab +[14:16:29] * S1/snps.txt +[14:16:29] * S1/snps.vcf +[14:16:29] * S1/snps.vcf.gz +[14:16:29] * S1/snps.vcf.gz.csi +[14:16:29] Walltime used: 4 seconds +[14:16:29] Did you know? Snippy is a combination of SNP, Skippy, and snappy. +[14:16:29] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2630,59 +2666,59 @@ [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq -[18:37:32] This is snippy 4.6.0 -[18:37:32] Written by Torsten Seemann -[18:37:32] Obtained from https://github.com/tseemann/snippy -[18:37:32] Detected operating system: linux -[18:37:32] Enabling bundled linux tools. -[18:37:32] Found bwa - /usr/bin/bwa -[18:37:32] Found bcftools - /usr/bin/bcftools -[18:37:32] Found samtools - /usr/bin/samtools -[18:37:32] Found java - /usr/bin/java -[18:37:32] Found snpEff - /usr/bin/snpEff -[18:37:32] Found samclip - /usr/bin/samclip -[18:37:32] Found seqtk - /usr/bin/seqtk -[18:37:32] Found parallel - /usr/bin/parallel -[18:37:32] Found freebayes - /usr/bin/freebayes -[18:37:33] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[18:37:33] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[18:37:33] Found vcfstreamsort - /usr/bin/vcfstreamsort -[18:37:33] Found vcfuniq - /usr/bin/vcfuniq -[18:37:33] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[18:37:33] Found gzip - /usr/bin/gzip -[18:37:33] Found vt - /usr/bin/vt -[18:37:33] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[18:37:33] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[18:37:33] Checking version: samtools --version is >= 1.7 - ok, have 1.21 -[18:37:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 -[18:37:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[18:37:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[18:37:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[18:37:34] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[18:37:34] Treating reference as 'fasta' format. -[18:37:34] Will use 2 CPU cores. -[18:37:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq -[18:37:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[18:37:34] Used --force, will overwrite existing S2 -[18:37:34] Changing working directory: S2 -[18:37:34] Creating reference folder: reference -[18:37:34] Extracting FASTA and GFF from reference. -[18:37:34] Wrote 3 sequences to ref.fa -[18:37:34] Wrote 0 features to ref.gff -[18:37:34] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[18:37:34] Using BAM RG (Read Group) ID: S2 -[18:37:34] Running: samtools faidx reference/ref.fa 2>> snps.log -[18:37:34] Running: bwa index reference/ref.fa 2>> snps.log -[18:37:34] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[18:37:34] Running: ln -sf reference/ref.fa . 2>> snps.log -[18:37:34] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[18:37:34] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[18:37:34] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[14:16:29] This is snippy 4.6.0 +[14:16:29] Written by Torsten Seemann +[14:16:29] Obtained from https://github.com/tseemann/snippy +[14:16:29] Detected operating system: linux +[14:16:29] Enabling bundled linux tools. +[14:16:29] Found bwa - /usr/bin/bwa +[14:16:29] Found bcftools - /usr/bin/bcftools +[14:16:29] Found samtools - /usr/bin/samtools +[14:16:29] Found java - /usr/bin/java +[14:16:29] Found snpEff - /usr/bin/snpEff +[14:16:29] Found samclip - /usr/bin/samclip +[14:16:29] Found seqtk - /usr/bin/seqtk +[14:16:29] Found parallel - /usr/bin/parallel +[14:16:29] Found freebayes - /usr/bin/freebayes +[14:16:29] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[14:16:29] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[14:16:29] Found vcfstreamsort - /usr/bin/vcfstreamsort +[14:16:29] Found vcfuniq - /usr/bin/vcfuniq +[14:16:29] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[14:16:29] Found gzip - /usr/bin/gzip +[14:16:29] Found vt - /usr/bin/vt +[14:16:29] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[14:16:29] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[14:16:29] Checking version: samtools --version is >= 1.7 - ok, have 1.21 +[14:16:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 +[14:16:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[14:16:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[14:16:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[14:16:30] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[14:16:30] Treating reference as 'fasta' format. +[14:16:30] Will use 2 CPU cores. +[14:16:30] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq +[14:16:30] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq +[14:16:30] Used --force, will overwrite existing S2 +[14:16:30] Changing working directory: S2 +[14:16:30] Creating reference folder: reference +[14:16:30] Extracting FASTA and GFF from reference. +[14:16:30] Wrote 3 sequences to ref.fa +[14:16:30] Wrote 0 features to ref.gff +[14:16:30] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[14:16:30] Using BAM RG (Read Group) ID: S2 +[14:16:30] Running: samtools faidx reference/ref.fa 2>> snps.log +[14:16:30] Running: bwa index reference/ref.fa 2>> snps.log +[14:16:30] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[14:16:30] Running: ln -sf reference/ref.fa . 2>> snps.log +[14:16:30] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[14:16:30] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[14:16:30] Running: bwa mem -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs +[M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai -[M::process] read 24000 sequences (2400000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11598, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... @@ -2692,17 +2728,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 433) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 1.255 CPU sec, 1.901 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.424 CPU sec, 0.714 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[main] Real time: 2.102 sec; CPU: 1.282 sec +[main] Real time: 0.863 sec; CPU: 1.487 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. -[18:37:37] Running: samtools index snps.bam 2>> snps.log -[18:37:37] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[18:37:37] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[18:37:41] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[14:16:31] Running: samtools index snps.bam 2>> snps.log +[14:16:31] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[14:16:31] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[14:16:33] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -2737,45 +2773,45 @@ total no. variants observed : 246 total no. reference observed : 0 -Time elapsed: 0.00s +Time elapsed: 0.01s -[18:37:41] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[18:37:41] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[18:37:41] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[18:37:41] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[18:37:41] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[18:37:41] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[18:37:41] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[18:37:41] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[18:37:41] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[18:37:41] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[18:37:41] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[18:37:42] Marked 841 heterozygous sites with 'n' -[18:37:42] Creating extra output files: BED GFF CSV TXT HTML -[18:37:42] Identified 246 variants. -[18:37:42] Result folder: S2 -[18:37:42] Result files: -[18:37:42] * S2/snps.aligned.fa -[18:37:42] * S2/snps.bam -[18:37:42] * S2/snps.bam.bai -[18:37:42] * S2/snps.bed -[18:37:42] * S2/snps.consensus.fa -[18:37:42] * S2/snps.consensus.subs.fa -[18:37:42] * S2/snps.csv -[18:37:42] * S2/snps.filt.vcf -[18:37:42] * S2/snps.gff -[18:37:42] * S2/snps.html -[18:37:42] * S2/snps.log -[18:37:42] * S2/snps.raw.vcf -[18:37:42] * S2/snps.subs.vcf -[18:37:42] * S2/snps.tab -[18:37:42] * S2/snps.txt -[18:37:42] * S2/snps.vcf -[18:37:42] * S2/snps.vcf.gz -[18:37:42] * S2/snps.vcf.gz.csi -[18:37:42] Walltime used: 10 seconds -[18:37:42] May the SNPs be with you. -[18:37:42] Done. +[14:16:33] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[14:16:33] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[14:16:33] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[14:16:33] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[14:16:33] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[14:16:33] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[14:16:33] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[14:16:33] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[14:16:33] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[14:16:33] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[14:16:33] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[14:16:33] Marked 841 heterozygous sites with 'n' +[14:16:33] Creating extra output files: BED GFF CSV TXT HTML +[14:16:33] Identified 246 variants. +[14:16:33] Result folder: S2 +[14:16:33] Result files: +[14:16:33] * S2/snps.aligned.fa +[14:16:33] * S2/snps.bam +[14:16:33] * S2/snps.bam.bai +[14:16:33] * S2/snps.bed +[14:16:33] * S2/snps.consensus.fa +[14:16:33] * S2/snps.consensus.subs.fa +[14:16:33] * S2/snps.csv +[14:16:33] * S2/snps.filt.vcf +[14:16:33] * S2/snps.gff +[14:16:33] * S2/snps.html +[14:16:33] * S2/snps.log +[14:16:33] * S2/snps.raw.vcf +[14:16:33] * S2/snps.subs.vcf +[14:16:33] * S2/snps.tab +[14:16:33] * S2/snps.txt +[14:16:33] * S2/snps.vcf +[14:16:33] * S2/snps.vcf.gz +[14:16:33] * S2/snps.vcf.gz.csi +[14:16:33] Walltime used: 4 seconds +[14:16:33] Questionable SNP? Try the --report option to see the alignments. +[14:16:33] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2784,59 +2820,59 @@ [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq -[18:37:43] This is snippy 4.6.0 -[18:37:43] Written by Torsten Seemann -[18:37:43] Obtained from https://github.com/tseemann/snippy -[18:37:43] Detected operating system: linux -[18:37:43] Enabling bundled linux tools. -[18:37:43] Found bwa - /usr/bin/bwa -[18:37:43] Found bcftools - /usr/bin/bcftools -[18:37:43] Found samtools - /usr/bin/samtools -[18:37:43] Found java - /usr/bin/java -[18:37:43] Found snpEff - /usr/bin/snpEff -[18:37:43] Found samclip - /usr/bin/samclip -[18:37:43] Found seqtk - /usr/bin/seqtk -[18:37:43] Found parallel - /usr/bin/parallel -[18:37:43] Found freebayes - /usr/bin/freebayes -[18:37:43] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[18:37:43] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[18:37:43] Found vcfstreamsort - /usr/bin/vcfstreamsort -[18:37:43] Found vcfuniq - /usr/bin/vcfuniq -[18:37:43] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[18:37:43] Found gzip - /usr/bin/gzip -[18:37:43] Found vt - /usr/bin/vt -[18:37:43] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[18:37:44] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[18:37:44] Checking version: samtools --version is >= 1.7 - ok, have 1.21 -[18:37:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 -[18:37:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[18:37:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[18:37:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[18:37:44] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[18:37:44] Treating reference as 'fasta' format. -[18:37:44] Will use 2 CPU cores. -[18:37:44] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq -[18:37:44] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[18:37:44] Used --force, will overwrite existing S3 -[18:37:44] Changing working directory: S3 -[18:37:44] Creating reference folder: reference -[18:37:44] Extracting FASTA and GFF from reference. -[18:37:44] Wrote 3 sequences to ref.fa -[18:37:44] Wrote 0 features to ref.gff -[18:37:44] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[18:37:44] Using BAM RG (Read Group) ID: S3 -[18:37:44] Running: samtools faidx reference/ref.fa 2>> snps.log -[18:37:44] Running: bwa index reference/ref.fa 2>> snps.log -[18:37:45] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[18:37:45] Running: ln -sf reference/ref.fa . 2>> snps.log -[18:37:45] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[18:37:45] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[18:37:45] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[14:16:34] This is snippy 4.6.0 +[14:16:34] Written by Torsten Seemann +[14:16:34] Obtained from https://github.com/tseemann/snippy +[14:16:34] Detected operating system: linux +[14:16:34] Enabling bundled linux tools. +[14:16:34] Found bwa - /usr/bin/bwa +[14:16:34] Found bcftools - /usr/bin/bcftools +[14:16:34] Found samtools - /usr/bin/samtools +[14:16:34] Found java - /usr/bin/java +[14:16:34] Found snpEff - /usr/bin/snpEff +[14:16:34] Found samclip - /usr/bin/samclip +[14:16:34] Found seqtk - /usr/bin/seqtk +[14:16:34] Found parallel - /usr/bin/parallel +[14:16:34] Found freebayes - /usr/bin/freebayes +[14:16:34] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[14:16:34] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[14:16:34] Found vcfstreamsort - /usr/bin/vcfstreamsort +[14:16:34] Found vcfuniq - /usr/bin/vcfuniq +[14:16:34] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[14:16:34] Found gzip - /usr/bin/gzip +[14:16:34] Found vt - /usr/bin/vt +[14:16:34] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[14:16:34] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[14:16:34] Checking version: samtools --version is >= 1.7 - ok, have 1.21 +[14:16:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 +[14:16:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[14:16:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[14:16:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[14:16:34] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[14:16:34] Treating reference as 'fasta' format. +[14:16:34] Will use 2 CPU cores. +[14:16:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq +[14:16:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq +[14:16:34] Used --force, will overwrite existing S3 +[14:16:34] Changing working directory: S3 +[14:16:34] Creating reference folder: reference +[14:16:34] Extracting FASTA and GFF from reference. +[14:16:34] Wrote 3 sequences to ref.fa +[14:16:34] Wrote 0 features to ref.gff +[14:16:34] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[14:16:34] Using BAM RG (Read Group) ID: S3 +[14:16:34] Running: samtools faidx reference/ref.fa 2>> snps.log +[14:16:34] Running: bwa index reference/ref.fa 2>> snps.log +[14:16:34] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[14:16:34] Running: ln -sf reference/ref.fa . 2>> snps.log +[14:16:34] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[14:16:34] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[14:16:34] Running: bwa mem -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs +[M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) [samclip] Loading: reference/ref.fa.fai [samclip] Found 3 sequences in reference/ref.fa.fai -[M::process] read 24000 sequences (2400000 bp)... [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0) [M::mem_pestat] skip orientation FF as there are not enough pairs [M::mem_pestat] analyzing insert size distribution for orientation FR... @@ -2846,17 +2882,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 436) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 1.262 CPU sec, 2.236 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.375 CPU sec, 0.689 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[main] Real time: 2.496 sec; CPU: 1.287 sec +[main] Real time: 0.869 sec; CPU: 1.445 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. -[18:37:48] Running: samtools index snps.bam 2>> snps.log -[18:37:48] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[18:37:48] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[18:37:51] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[14:16:36] Running: samtools index snps.bam 2>> snps.log +[14:16:36] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[14:16:36] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[14:16:37] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -2891,45 +2927,45 @@ total no. variants observed : 254 total no. reference observed : 0 -Time elapsed: 0.00s +Time elapsed: 0.01s -[18:37:51] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[18:37:52] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[18:37:52] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[18:37:52] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[18:37:52] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[18:37:52] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[18:37:52] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[18:37:52] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[18:37:52] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[18:37:52] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[18:37:52] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[18:37:53] Marked 846 heterozygous sites with 'n' -[18:37:53] Creating extra output files: BED GFF CSV TXT HTML -[18:37:53] Identified 254 variants. -[18:37:53] Result folder: S3 -[18:37:53] Result files: -[18:37:53] * S3/snps.aligned.fa -[18:37:53] * S3/snps.bam -[18:37:53] * S3/snps.bam.bai -[18:37:53] * S3/snps.bed -[18:37:53] * S3/snps.consensus.fa -[18:37:53] * S3/snps.consensus.subs.fa -[18:37:53] * S3/snps.csv -[18:37:53] * S3/snps.filt.vcf -[18:37:53] * S3/snps.gff -[18:37:53] * S3/snps.html -[18:37:53] * S3/snps.log -[18:37:53] * S3/snps.raw.vcf -[18:37:53] * S3/snps.subs.vcf -[18:37:53] * S3/snps.tab -[18:37:53] * S3/snps.txt -[18:37:53] * S3/snps.vcf -[18:37:53] * S3/snps.vcf.gz -[18:37:53] * S3/snps.vcf.gz.csi -[18:37:53] Walltime used: 10 seconds -[18:37:53] Did you know? Snippy is a combination of SNP, Skippy, and snappy. -[18:37:53] Done. +[14:16:37] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[14:16:37] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[14:16:37] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[14:16:37] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[14:16:37] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[14:16:37] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[14:16:37] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[14:16:38] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[14:16:38] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[14:16:38] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[14:16:38] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[14:16:38] Marked 846 heterozygous sites with 'n' +[14:16:38] Creating extra output files: BED GFF CSV TXT HTML +[14:16:38] Identified 254 variants. +[14:16:38] Result folder: S3 +[14:16:38] Result files: +[14:16:38] * S3/snps.aligned.fa +[14:16:38] * S3/snps.bam +[14:16:38] * S3/snps.bam.bai +[14:16:38] * S3/snps.bed +[14:16:38] * S3/snps.consensus.fa +[14:16:38] * S3/snps.consensus.subs.fa +[14:16:38] * S3/snps.csv +[14:16:38] * S3/snps.filt.vcf +[14:16:38] * S3/snps.gff +[14:16:38] * S3/snps.html +[14:16:38] * S3/snps.log +[14:16:38] * S3/snps.raw.vcf +[14:16:38] * S3/snps.subs.vcf +[14:16:38] * S3/snps.tab +[14:16:38] * S3/snps.txt +[14:16:38] * S3/snps.vcf +[14:16:38] * S3/snps.vcf.gz +[14:16:38] * S3/snps.vcf.gz.csi +[14:16:38] Walltime used: 4 seconds +[14:16:38] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues +[14:16:38] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2938,54 +2974,54 @@ [wgsim_core] calculating the total length of the reference sequence... [wgsim_core] 3 sequences, total length: 317336 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq -[18:37:53] This is snippy 4.6.0 -[18:37:53] Written by Torsten Seemann -[18:37:53] Obtained from https://github.com/tseemann/snippy -[18:37:53] Detected operating system: linux -[18:37:53] Enabling bundled linux tools. -[18:37:53] Found bwa - /usr/bin/bwa -[18:37:53] Found bcftools - /usr/bin/bcftools -[18:37:53] Found samtools - /usr/bin/samtools -[18:37:53] Found java - /usr/bin/java -[18:37:53] Found snpEff - /usr/bin/snpEff -[18:37:53] Found samclip - /usr/bin/samclip -[18:37:53] Found seqtk - /usr/bin/seqtk -[18:37:53] Found parallel - /usr/bin/parallel -[18:37:53] Found freebayes - /usr/bin/freebayes -[18:37:53] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[18:37:53] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[18:37:53] Found vcfstreamsort - /usr/bin/vcfstreamsort -[18:37:53] Found vcfuniq - /usr/bin/vcfuniq -[18:37:53] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[18:37:53] Found gzip - /usr/bin/gzip -[18:37:53] Found vt - /usr/bin/vt -[18:37:53] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[18:37:54] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[18:37:54] Checking version: samtools --version is >= 1.7 - ok, have 1.21 -[18:37:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 -[18:37:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[18:37:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[18:37:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[18:37:54] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[18:37:54] Treating reference as 'fasta' format. -[18:37:54] Will use 2 CPU cores. -[18:37:54] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq -[18:37:54] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq -[18:37:54] Used --force, will overwrite existing S4 -[18:37:54] Changing working directory: S4 -[18:37:54] Creating reference folder: reference -[18:37:54] Extracting FASTA and GFF from reference. -[18:37:54] Wrote 3 sequences to ref.fa -[18:37:54] Wrote 0 features to ref.gff -[18:37:54] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[18:37:54] Using BAM RG (Read Group) ID: S4 -[18:37:54] Running: samtools faidx reference/ref.fa 2>> snps.log -[18:37:54] Running: bwa index reference/ref.fa 2>> snps.log -[18:37:54] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[18:37:54] Running: ln -sf reference/ref.fa . 2>> snps.log -[18:37:55] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[18:37:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[18:37:55] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log +[14:16:38] This is snippy 4.6.0 +[14:16:38] Written by Torsten Seemann +[14:16:38] Obtained from https://github.com/tseemann/snippy +[14:16:38] Detected operating system: linux +[14:16:38] Enabling bundled linux tools. +[14:16:38] Found bwa - /usr/bin/bwa +[14:16:38] Found bcftools - /usr/bin/bcftools +[14:16:38] Found samtools - /usr/bin/samtools +[14:16:38] Found java - /usr/bin/java +[14:16:38] Found snpEff - /usr/bin/snpEff +[14:16:38] Found samclip - /usr/bin/samclip +[14:16:38] Found seqtk - /usr/bin/seqtk +[14:16:38] Found parallel - /usr/bin/parallel +[14:16:38] Found freebayes - /usr/bin/freebayes +[14:16:38] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[14:16:38] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[14:16:38] Found vcfstreamsort - /usr/bin/vcfstreamsort +[14:16:38] Found vcfuniq - /usr/bin/vcfuniq +[14:16:38] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[14:16:38] Found gzip - /usr/bin/gzip +[14:16:38] Found vt - /usr/bin/vt +[14:16:38] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[14:16:38] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[14:16:38] Checking version: samtools --version is >= 1.7 - ok, have 1.21 +[14:16:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.21 +[14:16:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[14:16:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[14:16:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[14:16:38] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[14:16:38] Treating reference as 'fasta' format. +[14:16:38] Will use 2 CPU cores. +[14:16:38] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq +[14:16:38] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq +[14:16:38] Used --force, will overwrite existing S4 +[14:16:38] Changing working directory: S4 +[14:16:38] Creating reference folder: reference +[14:16:38] Extracting FASTA and GFF from reference. +[14:16:39] Wrote 3 sequences to ref.fa +[14:16:39] Wrote 0 features to ref.gff +[14:16:39] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[14:16:39] Using BAM RG (Read Group) ID: S4 +[14:16:39] Running: samtools faidx reference/ref.fa 2>> snps.log +[14:16:39] Running: bwa index reference/ref.fa 2>> snps.log +[14:16:39] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[14:16:39] Running: ln -sf reference/ref.fa . 2>> snps.log +[14:16:39] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[14:16:39] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[14:16:39] Running: bwa mem -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::process] read 24000 sequences (2400000 bp)... [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann) @@ -3000,17 +3036,17 @@ [M::mem_pestat] low and high boundaries for proper pairs: (1, 425) [M::mem_pestat] skip orientation RF as there are not enough pairs [M::mem_pestat] skip orientation RR as there are not enough pairs -[M::mem_process_seqs] Processed 24000 reads in 1.226 CPU sec, 1.230 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.466 CPU sec, 0.737 real sec [main] Version: 0.7.18-r1243-dirty [main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq -[main] Real time: 1.563 sec; CPU: 1.252 sec +[main] Real time: 0.834 sec; CPU: 1.530 sec [samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. -[18:37:57] Running: samtools index snps.bam 2>> snps.log -[18:37:57] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[18:37:57] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log -[18:38:00] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log +[14:16:40] Running: samtools index snps.bam 2>> snps.log +[14:16:40] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[14:16:40] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log +[14:16:42] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log normalize v0.5 options: input VCF file - @@ -3045,45 +3081,45 @@ total no. variants observed : 257 total no. reference observed : 0 -Time elapsed: 0.00s +Time elapsed: 0.01s -[18:38:00] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[18:38:00] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log -[18:38:00] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[18:38:00] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[18:38:00] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[18:38:00] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[18:38:00] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[18:38:00] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[18:38:00] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[18:38:00] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[18:38:00] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[18:38:01] Marked 799 heterozygous sites with 'n' -[18:38:01] Creating extra output files: BED GFF CSV TXT HTML -[18:38:01] Identified 257 variants. -[18:38:01] Result folder: S4 -[18:38:01] Result files: -[18:38:01] * S4/snps.aligned.fa -[18:38:01] * S4/snps.bam -[18:38:01] * S4/snps.bam.bai -[18:38:01] * S4/snps.bed -[18:38:01] * S4/snps.consensus.fa -[18:38:01] * S4/snps.consensus.subs.fa -[18:38:01] * S4/snps.csv -[18:38:01] * S4/snps.filt.vcf -[18:38:01] * S4/snps.gff -[18:38:01] * S4/snps.html -[18:38:01] * S4/snps.log -[18:38:01] * S4/snps.raw.vcf -[18:38:01] * S4/snps.subs.vcf -[18:38:01] * S4/snps.tab -[18:38:01] * S4/snps.txt -[18:38:01] * S4/snps.vcf -[18:38:01] * S4/snps.vcf.gz -[18:38:01] * S4/snps.vcf.gz.csi -[18:38:01] Walltime used: 8 seconds -[18:38:01] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues -[18:38:01] Done. +[14:16:42] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[14:16:42] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log +[14:16:42] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[14:16:42] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[14:16:42] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[14:16:42] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[14:16:42] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[14:16:42] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[14:16:42] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[14:16:42] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[14:16:42] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[14:16:42] Marked 799 heterozygous sites with 'n' +[14:16:42] Creating extra output files: BED GFF CSV TXT HTML +[14:16:42] Identified 257 variants. +[14:16:42] Result folder: S4 +[14:16:42] Result files: +[14:16:42] * S4/snps.aligned.fa +[14:16:42] * S4/snps.bam +[14:16:42] * S4/snps.bam.bai +[14:16:42] * S4/snps.bed +[14:16:42] * S4/snps.consensus.fa +[14:16:42] * S4/snps.consensus.subs.fa +[14:16:42] * S4/snps.csv +[14:16:42] * S4/snps.filt.vcf +[14:16:42] * S4/snps.gff +[14:16:42] * S4/snps.html +[14:16:42] * S4/snps.log +[14:16:42] * S4/snps.raw.vcf +[14:16:42] * S4/snps.subs.vcf +[14:16:42] * S4/snps.tab +[14:16:42] * S4/snps.txt +[14:16:42] * S4/snps.vcf +[14:16:42] * S4/snps.vcf.gz +[14:16:42] * S4/snps.vcf.gz.csi +[14:16:42] Walltime used: 4 seconds +[14:16:42] Did you know? Snippy is a combination of SNP, Skippy, and snappy. +[14:16:42] Done. ../bin/snippy-core --prefix core --ref example.fna S1 S2 S3 S4 ../bin/snippy-core --prefix core-mask --ref example.fna --mask example.bed S1 S2 S3 S4 This is snippy-core 4.6.0 @@ -3116,7 +3152,7 @@ Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln -You can mask columns using '--mask BEDFILE --mask-char X' +The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy @@ -3150,7 +3186,7 @@ Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln -You can mask columns using '--mask BEDFILE --mask-char X' +The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md Done. wc -l S?/snps.tab 262 S1/snps.tab @@ -3188,12 +3224,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/671649/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/671649/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/1272158 and its subdirectories -I: Current time: Thu Mar 26 18:38:11 -12 2026 -I: pbuilder-time-stamp: 1774593491 +I: removing directory /srv/workspace/pbuilder/671649 and its subdirectories +I: Current time: Sat Feb 22 14:16:48 +14 2025 +I: pbuilder-time-stamp: 1740183408