Diff of the two buildlogs: -- --- b1/build.log 2024-12-31 21:06:45.600971091 +0000 +++ b2/build.log 2024-12-31 21:08:32.900081944 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Dec 31 09:05:15 -12 2024 -I: pbuilder-time-stamp: 1735679115 +I: Current time: Tue Feb 3 17:29:49 +14 2026 +I: pbuilder-time-stamp: 1770089389 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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/2933089/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/17200/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-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 3 03:29 /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/17200/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/17200/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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='3d74c02cafbc4e3db88ef23507d1ef10' - 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='2933089' - PS1='# ' - PS2='> ' + INVOCATION_ID=f5b1df5233af4240ba0813305db23e67 + 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=17200 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.q7ZAMuxm/pbuilderrc_4pzh --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.q7ZAMuxm/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.q7ZAMuxm/pbuilderrc_66Dz --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.q7ZAMuxm/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 codethink02-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/2933089/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/17200/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 unstable/main arm64 snp-sites arm64 2.5.1-2+b2 [14.0 kB] Get: 415 http://deb.debian.org/debian unstable/main arm64 snpeff all 5.2.e+dfsg-1 [7200 B] Get: 416 http://deb.debian.org/debian unstable/main arm64 vt arm64 0.57721+ds-3+b2 [720 kB] -Fetched 314 MB in 4s (88.5 MB/s) +Fetched 314 MB in 2s (180 MB/s) Preconfiguring packages ... Selecting previously unselected package libapparmor1: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 ... 19975 files and directories currently installed.) @@ -1919,8 +1951,8 @@ Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' -Local time is now: Tue Dec 31 21:06:09 UTC 2024. -Universal Time is now: Tue Dec 31 21:06:09 UTC 2024. +Local time is now: Tue Feb 3 03:30:48 UTC 2026. +Universal Time is now: Tue Feb 3 03:30:48 UTC 2026. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -2449,7 +2481,11 @@ 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/17200/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/17200/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 @@ -2475,54 +2511,54 @@ [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 -[09:06:22] This is snippy 4.6.0 -[09:06:22] Written by Torsten Seemann -[09:06:22] Obtained from https://github.com/tseemann/snippy -[09:06:22] Detected operating system: linux -[09:06:22] Enabling bundled linux tools. -[09:06:22] Found bwa - /usr/bin/bwa -[09:06:22] Found bcftools - /usr/bin/bcftools -[09:06:22] Found samtools - /usr/bin/samtools -[09:06:22] Found java - /usr/bin/java -[09:06:22] Found snpEff - /usr/bin/snpEff -[09:06:22] Found samclip - /usr/bin/samclip -[09:06:22] Found seqtk - /usr/bin/seqtk -[09:06:22] Found parallel - /usr/bin/parallel -[09:06:23] Found freebayes - /usr/bin/freebayes -[09:06:23] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[09:06:23] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[09:06:23] Found vcfstreamsort - /usr/bin/vcfstreamsort -[09:06:23] Found vcfuniq - /usr/bin/vcfuniq -[09:06:23] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[09:06:23] Found gzip - /usr/bin/gzip -[09:06:23] Found vt - /usr/bin/vt -[09:06:23] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[09:06:23] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[09:06:23] Checking version: samtools --version is >= 1.7 - ok, have 1.20 -[09:06:23] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[09:06:23] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[09:06:23] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[09:06:23] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[09:06:23] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[09:06:23] Treating reference as 'fasta' format. -[09:06:23] Will use 2 CPU cores. -[09:06:23] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq -[09:06:23] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[09:06:23] Used --force, will overwrite existing S1 -[09:06:23] Changing working directory: S1 -[09:06:23] Creating reference folder: reference -[09:06:23] Extracting FASTA and GFF from reference. -[09:06:23] Wrote 3 sequences to ref.fa -[09:06:23] Wrote 0 features to ref.gff -[09:06:23] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[09:06:23] Using BAM RG (Read Group) ID: S1 -[09:06:23] Running: samtools faidx reference/ref.fa 2>> snps.log -[09:06:23] Running: bwa index reference/ref.fa 2>> snps.log -[09:06:23] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[09:06:23] Running: ln -sf reference/ref.fa . 2>> snps.log -[09:06:23] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[09:06:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[09:06:23] 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 +[17:31:08] This is snippy 4.6.0 +[17:31:08] Written by Torsten Seemann +[17:31:08] Obtained from https://github.com/tseemann/snippy +[17:31:08] Detected operating system: linux +[17:31:08] Enabling bundled linux tools. +[17:31:08] Found bwa - /usr/bin/bwa +[17:31:08] Found bcftools - /usr/bin/bcftools +[17:31:08] Found samtools - /usr/bin/samtools +[17:31:08] Found java - /usr/bin/java +[17:31:08] Found snpEff - /usr/bin/snpEff +[17:31:08] Found samclip - /usr/bin/samclip +[17:31:08] Found seqtk - /usr/bin/seqtk +[17:31:08] Found parallel - /usr/bin/parallel +[17:31:08] Found freebayes - /usr/bin/freebayes +[17:31:08] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[17:31:08] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[17:31:08] Found vcfstreamsort - /usr/bin/vcfstreamsort +[17:31:08] Found vcfuniq - /usr/bin/vcfuniq +[17:31:08] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[17:31:08] Found gzip - /usr/bin/gzip +[17:31:08] Found vt - /usr/bin/vt +[17:31:08] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[17:31:08] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[17:31:08] Checking version: samtools --version is >= 1.7 - ok, have 1.20 +[17:31:08] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[17:31:08] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[17:31:08] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[17:31:08] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[17:31:08] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[17:31:08] Treating reference as 'fasta' format. +[17:31:08] Will use 2 CPU cores. +[17:31:08] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq +[17:31:08] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq +[17:31:08] Used --force, will overwrite existing S1 +[17:31:08] Changing working directory: S1 +[17:31:08] Creating reference folder: reference +[17:31:08] Extracting FASTA and GFF from reference. +[17:31:08] Wrote 3 sequences to ref.fa +[17:31:08] Wrote 0 features to ref.gff +[17:31:08] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[17:31:08] Using BAM RG (Read Group) ID: S1 +[17:31:08] Running: samtools faidx reference/ref.fa 2>> snps.log +[17:31:08] Running: bwa index reference/ref.fa 2>> snps.log +[17:31:08] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[17:31:08] Running: ln -sf reference/ref.fa . 2>> snps.log +[17:31:08] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[17:31:08] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[17:31:08] 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) @@ -2537,17 +2573,17 @@ [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 1.341 CPU sec, 0.673 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.395 CPU sec, 0.700 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: 0.767 sec; CPU: 1.406 sec +[main] Real time: 0.852 sec; CPU: 1.461 sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. -[09:06:24] Running: samtools index snps.bam 2>> snps.log -[09:06:24] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[09:06:24] 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 -[09:06:26] 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 +[17:31:10] Running: samtools index snps.bam 2>> snps.log +[17:31:10] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[17:31:10] 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 +[17:31:11] 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 - @@ -2584,43 +2620,43 @@ Time elapsed: 0.01s -[09:06:26] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[09:06:26] 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 -[09:06:26] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[09:06:26] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[09:06:26] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[09:06:26] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[09:06:26] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[09:06:26] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[09:06:26] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[09:06:26] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[09:06:26] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[09:06:26] Marked 749 heterozygous sites with 'n' -[09:06:26] Creating extra output files: BED GFF CSV TXT HTML -[09:06:26] Identified 261 variants. -[09:06:26] Result folder: S1 -[09:06:26] Result files: -[09:06:26] * S1/snps.aligned.fa -[09:06:26] * S1/snps.bam -[09:06:26] * S1/snps.bam.bai -[09:06:26] * S1/snps.bed -[09:06:26] * S1/snps.consensus.fa -[09:06:26] * S1/snps.consensus.subs.fa -[09:06:26] * S1/snps.csv -[09:06:26] * S1/snps.filt.vcf -[09:06:26] * S1/snps.gff -[09:06:26] * S1/snps.html -[09:06:26] * S1/snps.log -[09:06:26] * S1/snps.raw.vcf -[09:06:26] * S1/snps.subs.vcf -[09:06:26] * S1/snps.tab -[09:06:26] * S1/snps.txt -[09:06:26] * S1/snps.vcf -[09:06:26] * S1/snps.vcf.gz -[09:06:26] * S1/snps.vcf.gz.csi -[09:06:26] Walltime used: 4 seconds -[09:06:26] Wishing you a life free of homopolymer errors. -[09:06:26] Done. +[17:31:11] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[17:31:11] 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 +[17:31:12] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[17:31:12] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[17:31:12] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[17:31:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[17:31:12] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[17:31:12] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[17:31:12] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[17:31:12] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[17:31:12] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[17:31:12] Marked 749 heterozygous sites with 'n' +[17:31:12] Creating extra output files: BED GFF CSV TXT HTML +[17:31:12] Identified 261 variants. +[17:31:12] Result folder: S1 +[17:31:12] Result files: +[17:31:12] * S1/snps.aligned.fa +[17:31:12] * S1/snps.bam +[17:31:12] * S1/snps.bam.bai +[17:31:12] * S1/snps.bed +[17:31:12] * S1/snps.consensus.fa +[17:31:12] * S1/snps.consensus.subs.fa +[17:31:12] * S1/snps.csv +[17:31:12] * S1/snps.filt.vcf +[17:31:12] * S1/snps.gff +[17:31:12] * S1/snps.html +[17:31:12] * S1/snps.log +[17:31:12] * S1/snps.raw.vcf +[17:31:12] * S1/snps.subs.vcf +[17:31:12] * S1/snps.tab +[17:31:12] * S1/snps.txt +[17:31:12] * S1/snps.vcf +[17:31:12] * S1/snps.vcf.gz +[17:31:12] * S1/snps.vcf.gz.csi +[17:31:12] Walltime used: 4 seconds +[17:31:12] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues +[17:31:12] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2629,54 +2665,54 @@ [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 S2 --R1 S2/R1.fq --R2 S2/R2.fq -[09:06:27] This is snippy 4.6.0 -[09:06:27] Written by Torsten Seemann -[09:06:27] Obtained from https://github.com/tseemann/snippy -[09:06:27] Detected operating system: linux -[09:06:27] Enabling bundled linux tools. -[09:06:27] Found bwa - /usr/bin/bwa -[09:06:27] Found bcftools - /usr/bin/bcftools -[09:06:27] Found samtools - /usr/bin/samtools -[09:06:27] Found java - /usr/bin/java -[09:06:27] Found snpEff - /usr/bin/snpEff -[09:06:27] Found samclip - /usr/bin/samclip -[09:06:27] Found seqtk - /usr/bin/seqtk -[09:06:27] Found parallel - /usr/bin/parallel -[09:06:27] Found freebayes - /usr/bin/freebayes -[09:06:27] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[09:06:27] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[09:06:27] Found vcfstreamsort - /usr/bin/vcfstreamsort -[09:06:27] Found vcfuniq - /usr/bin/vcfuniq -[09:06:27] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[09:06:27] Found gzip - /usr/bin/gzip -[09:06:27] Found vt - /usr/bin/vt -[09:06:27] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[09:06:27] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[09:06:27] Checking version: samtools --version is >= 1.7 - ok, have 1.20 -[09:06:27] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[09:06:27] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[09:06:27] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[09:06:27] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[09:06:27] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[09:06:27] Treating reference as 'fasta' format. -[09:06:27] Will use 2 CPU cores. -[09:06:27] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq -[09:06:27] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[09:06:27] Used --force, will overwrite existing S2 -[09:06:27] Changing working directory: S2 -[09:06:27] Creating reference folder: reference -[09:06:27] Extracting FASTA and GFF from reference. -[09:06:27] Wrote 3 sequences to ref.fa -[09:06:27] Wrote 0 features to ref.gff -[09:06:27] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[09:06:27] Using BAM RG (Read Group) ID: S2 -[09:06:27] Running: samtools faidx reference/ref.fa 2>> snps.log -[09:06:27] Running: bwa index reference/ref.fa 2>> snps.log -[09:06:27] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[09:06:27] Running: ln -sf reference/ref.fa . 2>> snps.log -[09:06:27] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[09:06:27] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[09:06:27] 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 +[17:31:12] This is snippy 4.6.0 +[17:31:12] Written by Torsten Seemann +[17:31:12] Obtained from https://github.com/tseemann/snippy +[17:31:12] Detected operating system: linux +[17:31:12] Enabling bundled linux tools. +[17:31:12] Found bwa - /usr/bin/bwa +[17:31:12] Found bcftools - /usr/bin/bcftools +[17:31:12] Found samtools - /usr/bin/samtools +[17:31:12] Found java - /usr/bin/java +[17:31:12] Found snpEff - /usr/bin/snpEff +[17:31:12] Found samclip - /usr/bin/samclip +[17:31:12] Found seqtk - /usr/bin/seqtk +[17:31:12] Found parallel - /usr/bin/parallel +[17:31:12] Found freebayes - /usr/bin/freebayes +[17:31:12] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[17:31:12] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[17:31:12] Found vcfstreamsort - /usr/bin/vcfstreamsort +[17:31:12] Found vcfuniq - /usr/bin/vcfuniq +[17:31:12] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[17:31:12] Found gzip - /usr/bin/gzip +[17:31:12] Found vt - /usr/bin/vt +[17:31:12] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[17:31:12] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[17:31:12] Checking version: samtools --version is >= 1.7 - ok, have 1.20 +[17:31:12] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[17:31:12] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[17:31:13] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[17:31:13] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[17:31:13] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[17:31:13] Treating reference as 'fasta' format. +[17:31:13] Will use 2 CPU cores. +[17:31:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq +[17:31:13] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq +[17:31:13] Used --force, will overwrite existing S2 +[17:31:13] Changing working directory: S2 +[17:31:13] Creating reference folder: reference +[17:31:13] Extracting FASTA and GFF from reference. +[17:31:13] Wrote 3 sequences to ref.fa +[17:31:13] Wrote 0 features to ref.gff +[17:31:13] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[17:31:13] Using BAM RG (Read Group) ID: S2 +[17:31:13] Running: samtools faidx reference/ref.fa 2>> snps.log +[17:31:13] Running: bwa index reference/ref.fa 2>> snps.log +[17:31:13] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[17:31:13] Running: ln -sf reference/ref.fa . 2>> snps.log +[17:31:13] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[17:31:13] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[17:31:13] 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) @@ -2691,17 +2727,17 @@ [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 1.351 CPU sec, 0.678 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.375 CPU sec, 0.690 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: 0.830 sec; CPU: 1.415 sec +[main] Real time: 0.840 sec; CPU: 1.441 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. -[09:06:28] Running: samtools index snps.bam 2>> snps.log -[09:06:29] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[09:06:29] 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 -[09:06:30] 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 +[17:31:14] Running: samtools index snps.bam 2>> snps.log +[17:31:14] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[17:31:14] 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 +[17:31:16] 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 - @@ -2738,43 +2774,43 @@ Time elapsed: 0.01s -[09:06:30] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[09:06:30] 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 -[09:06:30] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[09:06:30] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[09:06:30] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[09:06:30] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[09:06:30] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[09:06:30] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[09:06:30] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[09:06:30] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[09:06:30] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[09:06:31] Marked 841 heterozygous sites with 'n' -[09:06:31] Creating extra output files: BED GFF CSV TXT HTML -[09:06:31] Identified 246 variants. -[09:06:31] Result folder: S2 -[09:06:31] Result files: -[09:06:31] * S2/snps.aligned.fa -[09:06:31] * S2/snps.bam -[09:06:31] * S2/snps.bam.bai -[09:06:31] * S2/snps.bed -[09:06:31] * S2/snps.consensus.fa -[09:06:31] * S2/snps.consensus.subs.fa -[09:06:31] * S2/snps.csv -[09:06:31] * S2/snps.filt.vcf -[09:06:31] * S2/snps.gff -[09:06:31] * S2/snps.html -[09:06:31] * S2/snps.log -[09:06:31] * S2/snps.raw.vcf -[09:06:31] * S2/snps.subs.vcf -[09:06:31] * S2/snps.tab -[09:06:31] * S2/snps.txt -[09:06:31] * S2/snps.vcf -[09:06:31] * S2/snps.vcf.gz -[09:06:31] * S2/snps.vcf.gz.csi -[09:06:31] Walltime used: 4 seconds -[09:06:31] Questionable SNP? Try the --report option to see the alignments. -[09:06:31] Done. +[17:31:16] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[17:31:16] 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 +[17:31:16] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[17:31:16] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[17:31:16] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[17:31:16] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[17:31:16] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[17:31:16] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[17:31:16] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[17:31:16] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[17:31:16] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[17:31:16] Marked 841 heterozygous sites with 'n' +[17:31:16] Creating extra output files: BED GFF CSV TXT HTML +[17:31:16] Identified 246 variants. +[17:31:16] Result folder: S2 +[17:31:16] Result files: +[17:31:16] * S2/snps.aligned.fa +[17:31:16] * S2/snps.bam +[17:31:16] * S2/snps.bam.bai +[17:31:16] * S2/snps.bed +[17:31:16] * S2/snps.consensus.fa +[17:31:16] * S2/snps.consensus.subs.fa +[17:31:16] * S2/snps.csv +[17:31:16] * S2/snps.filt.vcf +[17:31:16] * S2/snps.gff +[17:31:16] * S2/snps.html +[17:31:16] * S2/snps.log +[17:31:16] * S2/snps.raw.vcf +[17:31:16] * S2/snps.subs.vcf +[17:31:16] * S2/snps.tab +[17:31:16] * S2/snps.txt +[17:31:16] * S2/snps.vcf +[17:31:16] * S2/snps.vcf.gz +[17:31:16] * S2/snps.vcf.gz.csi +[17:31:16] Walltime used: 4 seconds +[17:31:16] Wishing you a life free of homopolymer errors. +[17:31:16] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2783,54 +2819,54 @@ [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 S3 --R1 S3/R1.fq --R2 S3/R2.fq -[09:06:31] This is snippy 4.6.0 -[09:06:31] Written by Torsten Seemann -[09:06:31] Obtained from https://github.com/tseemann/snippy -[09:06:31] Detected operating system: linux -[09:06:31] Enabling bundled linux tools. -[09:06:31] Found bwa - /usr/bin/bwa -[09:06:31] Found bcftools - /usr/bin/bcftools -[09:06:31] Found samtools - /usr/bin/samtools -[09:06:31] Found java - /usr/bin/java -[09:06:31] Found snpEff - /usr/bin/snpEff -[09:06:31] Found samclip - /usr/bin/samclip -[09:06:31] Found seqtk - /usr/bin/seqtk -[09:06:31] Found parallel - /usr/bin/parallel -[09:06:31] Found freebayes - /usr/bin/freebayes -[09:06:31] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[09:06:31] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[09:06:31] Found vcfstreamsort - /usr/bin/vcfstreamsort -[09:06:31] Found vcfuniq - /usr/bin/vcfuniq -[09:06:31] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[09:06:31] Found gzip - /usr/bin/gzip -[09:06:31] Found vt - /usr/bin/vt -[09:06:31] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[09:06:31] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[09:06:31] Checking version: samtools --version is >= 1.7 - ok, have 1.20 -[09:06:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[09:06:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[09:06:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[09:06:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[09:06:31] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[09:06:31] Treating reference as 'fasta' format. -[09:06:31] Will use 2 CPU cores. -[09:06:31] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq -[09:06:31] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[09:06:31] Used --force, will overwrite existing S3 -[09:06:31] Changing working directory: S3 -[09:06:31] Creating reference folder: reference -[09:06:31] Extracting FASTA and GFF from reference. -[09:06:31] Wrote 3 sequences to ref.fa -[09:06:31] Wrote 0 features to ref.gff -[09:06:31] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[09:06:31] Using BAM RG (Read Group) ID: S3 -[09:06:31] Running: samtools faidx reference/ref.fa 2>> snps.log -[09:06:31] Running: bwa index reference/ref.fa 2>> snps.log -[09:06:31] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[09:06:31] Running: ln -sf reference/ref.fa . 2>> snps.log -[09:06:31] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[09:06:31] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[09:06:31] 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 +[17:31:17] This is snippy 4.6.0 +[17:31:17] Written by Torsten Seemann +[17:31:17] Obtained from https://github.com/tseemann/snippy +[17:31:17] Detected operating system: linux +[17:31:17] Enabling bundled linux tools. +[17:31:17] Found bwa - /usr/bin/bwa +[17:31:17] Found bcftools - /usr/bin/bcftools +[17:31:17] Found samtools - /usr/bin/samtools +[17:31:17] Found java - /usr/bin/java +[17:31:17] Found snpEff - /usr/bin/snpEff +[17:31:17] Found samclip - /usr/bin/samclip +[17:31:17] Found seqtk - /usr/bin/seqtk +[17:31:17] Found parallel - /usr/bin/parallel +[17:31:17] Found freebayes - /usr/bin/freebayes +[17:31:17] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[17:31:17] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[17:31:17] Found vcfstreamsort - /usr/bin/vcfstreamsort +[17:31:17] Found vcfuniq - /usr/bin/vcfuniq +[17:31:17] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[17:31:17] Found gzip - /usr/bin/gzip +[17:31:17] Found vt - /usr/bin/vt +[17:31:17] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[17:31:17] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[17:31:17] Checking version: samtools --version is >= 1.7 - ok, have 1.20 +[17:31:17] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[17:31:17] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[17:31:17] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[17:31:17] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[17:31:17] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[17:31:17] Treating reference as 'fasta' format. +[17:31:17] Will use 2 CPU cores. +[17:31:17] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq +[17:31:17] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq +[17:31:17] Used --force, will overwrite existing S3 +[17:31:17] Changing working directory: S3 +[17:31:17] Creating reference folder: reference +[17:31:17] Extracting FASTA and GFF from reference. +[17:31:17] Wrote 3 sequences to ref.fa +[17:31:17] Wrote 0 features to ref.gff +[17:31:17] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[17:31:17] Using BAM RG (Read Group) ID: S3 +[17:31:17] Running: samtools faidx reference/ref.fa 2>> snps.log +[17:31:17] Running: bwa index reference/ref.fa 2>> snps.log +[17:31:17] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[17:31:17] Running: ln -sf reference/ref.fa . 2>> snps.log +[17:31:17] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[17:31:17] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[17:31:17] 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) @@ -2845,17 +2881,17 @@ [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 1.300 CPU sec, 0.651 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.467 CPU sec, 0.737 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: 0.778 sec; CPU: 1.341 sec +[main] Real time: 0.890 sec; CPU: 1.533 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. -[09:06:33] Running: samtools index snps.bam 2>> snps.log -[09:06:33] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[09:06:33] 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 -[09:06:34] 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 +[17:31:19] Running: samtools index snps.bam 2>> snps.log +[17:31:19] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[17:31:19] 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 +[17:31:20] 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 - @@ -2890,45 +2926,45 @@ total no. variants observed : 254 total no. reference observed : 0 -Time elapsed: 0.00s +Time elapsed: 0.01s -[09:06:34] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[09:06:34] 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 -[09:06:34] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[09:06:34] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[09:06:34] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[09:06:34] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[09:06:34] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[09:06:34] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[09:06:34] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[09:06:34] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[09:06:34] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[09:06:35] Marked 846 heterozygous sites with 'n' -[09:06:35] Creating extra output files: BED GFF CSV TXT HTML -[09:06:35] Identified 254 variants. -[09:06:35] Result folder: S3 -[09:06:35] Result files: -[09:06:35] * S3/snps.aligned.fa -[09:06:35] * S3/snps.bam -[09:06:35] * S3/snps.bam.bai -[09:06:35] * S3/snps.bed -[09:06:35] * S3/snps.consensus.fa -[09:06:35] * S3/snps.consensus.subs.fa -[09:06:35] * S3/snps.csv -[09:06:35] * S3/snps.filt.vcf -[09:06:35] * S3/snps.gff -[09:06:35] * S3/snps.html -[09:06:35] * S3/snps.log -[09:06:35] * S3/snps.raw.vcf -[09:06:35] * S3/snps.subs.vcf -[09:06:35] * S3/snps.tab -[09:06:35] * S3/snps.txt -[09:06:35] * S3/snps.vcf -[09:06:35] * S3/snps.vcf.gz -[09:06:35] * S3/snps.vcf.gz.csi -[09:06:35] Walltime used: 4 seconds -[09:06:35] May the SNPs be with you. -[09:06:35] Done. +[17:31:20] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[17:31:20] 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 +[17:31:20] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[17:31:20] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[17:31:20] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[17:31:20] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[17:31:20] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[17:31:20] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[17:31:20] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[17:31:20] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[17:31:21] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[17:31:21] Marked 846 heterozygous sites with 'n' +[17:31:21] Creating extra output files: BED GFF CSV TXT HTML +[17:31:21] Identified 254 variants. +[17:31:21] Result folder: S3 +[17:31:21] Result files: +[17:31:21] * S3/snps.aligned.fa +[17:31:21] * S3/snps.bam +[17:31:21] * S3/snps.bam.bai +[17:31:21] * S3/snps.bed +[17:31:21] * S3/snps.consensus.fa +[17:31:21] * S3/snps.consensus.subs.fa +[17:31:21] * S3/snps.csv +[17:31:21] * S3/snps.filt.vcf +[17:31:21] * S3/snps.gff +[17:31:21] * S3/snps.html +[17:31:21] * S3/snps.log +[17:31:21] * S3/snps.raw.vcf +[17:31:21] * S3/snps.subs.vcf +[17:31:21] * S3/snps.tab +[17:31:21] * S3/snps.txt +[17:31:21] * S3/snps.vcf +[17:31:21] * S3/snps.vcf.gz +[17:31:21] * S3/snps.vcf.gz.csi +[17:31:21] Walltime used: 4 seconds +[17:31:21] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md +[17:31:21] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2937,54 +2973,54 @@ [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 -[09:06:35] This is snippy 4.6.0 -[09:06:35] Written by Torsten Seemann -[09:06:35] Obtained from https://github.com/tseemann/snippy -[09:06:35] Detected operating system: linux -[09:06:35] Enabling bundled linux tools. -[09:06:35] Found bwa - /usr/bin/bwa -[09:06:35] Found bcftools - /usr/bin/bcftools -[09:06:35] Found samtools - /usr/bin/samtools -[09:06:35] Found java - /usr/bin/java -[09:06:35] Found snpEff - /usr/bin/snpEff -[09:06:35] Found samclip - /usr/bin/samclip -[09:06:35] Found seqtk - /usr/bin/seqtk -[09:06:35] Found parallel - /usr/bin/parallel -[09:06:35] Found freebayes - /usr/bin/freebayes -[09:06:35] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[09:06:35] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[09:06:35] Found vcfstreamsort - /usr/bin/vcfstreamsort -[09:06:35] Found vcfuniq - /usr/bin/vcfuniq -[09:06:35] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[09:06:35] Found gzip - /usr/bin/gzip -[09:06:35] Found vt - /usr/bin/vt -[09:06:35] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[09:06:35] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[09:06:35] Checking version: samtools --version is >= 1.7 - ok, have 1.20 -[09:06:35] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 -[09:06:35] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 -[09:06:35] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[09:06:35] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 -[09:06:35] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[09:06:35] Treating reference as 'fasta' format. -[09:06:35] Will use 2 CPU cores. -[09:06:35] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq -[09:06:35] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq -[09:06:35] Used --force, will overwrite existing S4 -[09:06:35] Changing working directory: S4 -[09:06:35] Creating reference folder: reference -[09:06:35] Extracting FASTA and GFF from reference. -[09:06:35] Wrote 3 sequences to ref.fa -[09:06:35] Wrote 0 features to ref.gff -[09:06:35] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[09:06:35] Using BAM RG (Read Group) ID: S4 -[09:06:35] Running: samtools faidx reference/ref.fa 2>> snps.log -[09:06:35] Running: bwa index reference/ref.fa 2>> snps.log -[09:06:35] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[09:06:35] Running: ln -sf reference/ref.fa . 2>> snps.log -[09:06:35] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[09:06:35] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[09:06:35] 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 +[17:31:21] This is snippy 4.6.0 +[17:31:21] Written by Torsten Seemann +[17:31:21] Obtained from https://github.com/tseemann/snippy +[17:31:21] Detected operating system: linux +[17:31:21] Enabling bundled linux tools. +[17:31:21] Found bwa - /usr/bin/bwa +[17:31:21] Found bcftools - /usr/bin/bcftools +[17:31:21] Found samtools - /usr/bin/samtools +[17:31:21] Found java - /usr/bin/java +[17:31:21] Found snpEff - /usr/bin/snpEff +[17:31:21] Found samclip - /usr/bin/samclip +[17:31:21] Found seqtk - /usr/bin/seqtk +[17:31:21] Found parallel - /usr/bin/parallel +[17:31:21] Found freebayes - /usr/bin/freebayes +[17:31:21] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[17:31:21] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[17:31:21] Found vcfstreamsort - /usr/bin/vcfstreamsort +[17:31:21] Found vcfuniq - /usr/bin/vcfuniq +[17:31:21] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[17:31:21] Found gzip - /usr/bin/gzip +[17:31:21] Found vt - /usr/bin/vt +[17:31:21] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[17:31:21] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[17:31:21] Checking version: samtools --version is >= 1.7 - ok, have 1.20 +[17:31:21] Checking version: bcftools --version is >= 1.7 - ok, have 1.20 +[17:31:21] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.7 +[17:31:21] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[17:31:21] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18 +[17:31:21] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[17:31:21] Treating reference as 'fasta' format. +[17:31:21] Will use 2 CPU cores. +[17:31:21] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq +[17:31:21] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq +[17:31:21] Used --force, will overwrite existing S4 +[17:31:21] Changing working directory: S4 +[17:31:21] Creating reference folder: reference +[17:31:21] Extracting FASTA and GFF from reference. +[17:31:21] Wrote 3 sequences to ref.fa +[17:31:21] Wrote 0 features to ref.gff +[17:31:21] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[17:31:21] Using BAM RG (Read Group) ID: S4 +[17:31:21] Running: samtools faidx reference/ref.fa 2>> snps.log +[17:31:21] Running: bwa index reference/ref.fa 2>> snps.log +[17:31:22] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[17:31:22] Running: ln -sf reference/ref.fa . 2>> snps.log +[17:31:22] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[17:31:22] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[17:31:22] 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) @@ -2999,17 +3035,17 @@ [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 1.242 CPU sec, 0.624 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.478 CPU sec, 0.742 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: 0.760 sec; CPU: 1.287 sec +[main] Real time: 0.841 sec; CPU: 1.543 sec [samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. -[09:06:36] Running: samtools index snps.bam 2>> snps.log -[09:06:36] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[09:06:37] 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 -[09:06:38] 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 +[17:31:23] Running: samtools index snps.bam 2>> snps.log +[17:31:23] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[17:31:23] 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 +[17:31:25] 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 - @@ -3046,43 +3082,43 @@ Time elapsed: 0.01s -[09:06:38] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[09:06:38] 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 -[09:06:38] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[09:06:38] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[09:06:38] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[09:06:38] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[09:06:38] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[09:06:38] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[09:06:38] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[09:06:38] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[09:06:38] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[09:06:39] Marked 799 heterozygous sites with 'n' -[09:06:39] Creating extra output files: BED GFF CSV TXT HTML -[09:06:39] Identified 257 variants. -[09:06:39] Result folder: S4 -[09:06:39] Result files: -[09:06:39] * S4/snps.aligned.fa -[09:06:39] * S4/snps.bam -[09:06:39] * S4/snps.bam.bai -[09:06:39] * S4/snps.bed -[09:06:39] * S4/snps.consensus.fa -[09:06:39] * S4/snps.consensus.subs.fa -[09:06:39] * S4/snps.csv -[09:06:39] * S4/snps.filt.vcf -[09:06:39] * S4/snps.gff -[09:06:39] * S4/snps.html -[09:06:39] * S4/snps.log -[09:06:39] * S4/snps.raw.vcf -[09:06:39] * S4/snps.subs.vcf -[09:06:39] * S4/snps.tab -[09:06:39] * S4/snps.txt -[09:06:39] * S4/snps.vcf -[09:06:39] * S4/snps.vcf.gz -[09:06:39] * S4/snps.vcf.gz.csi -[09:06:39] Walltime used: 4 seconds -[09:06:39] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md -[09:06:39] Done. +[17:31:25] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[17:31:25] 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 +[17:31:25] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[17:31:25] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[17:31:25] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[17:31:25] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[17:31:25] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[17:31:25] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[17:31:25] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[17:31:25] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[17:31:25] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[17:31:25] Marked 799 heterozygous sites with 'n' +[17:31:25] Creating extra output files: BED GFF CSV TXT HTML +[17:31:25] Identified 257 variants. +[17:31:25] Result folder: S4 +[17:31:25] Result files: +[17:31:25] * S4/snps.aligned.fa +[17:31:25] * S4/snps.bam +[17:31:25] * S4/snps.bam.bai +[17:31:25] * S4/snps.bed +[17:31:25] * S4/snps.consensus.fa +[17:31:25] * S4/snps.consensus.subs.fa +[17:31:25] * S4/snps.csv +[17:31:25] * S4/snps.filt.vcf +[17:31:25] * S4/snps.gff +[17:31:25] * S4/snps.html +[17:31:25] * S4/snps.log +[17:31:25] * S4/snps.raw.vcf +[17:31:25] * S4/snps.subs.vcf +[17:31:25] * S4/snps.tab +[17:31:25] * S4/snps.txt +[17:31:25] * S4/snps.vcf +[17:31:25] * S4/snps.vcf.gz +[17:31:25] * S4/snps.vcf.gz.csi +[17:31:25] Walltime used: 4 seconds +[17:31:25] Questionable SNP? Try the --report option to see the alignments. +[17:31:25] 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 @@ -3115,7 +3151,7 @@ Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln -Found a bug? Post it at http://github.com/tseemann/snippy/issues +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 @@ -3149,7 +3185,7 @@ Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln -Have a suggestion? Tell me at http://github.com/tseemann/snippy/issues +The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md Done. wc -l S?/snps.tab 262 S1/snps.tab @@ -3187,12 +3223,14 @@ 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/17200/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/17200/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/2933089 and its subdirectories -I: Current time: Tue Dec 31 09:06:44 -12 2024 -I: pbuilder-time-stamp: 1735679204 +I: removing directory /srv/workspace/pbuilder/17200 and its subdirectories +I: Current time: Tue Feb 3 17:31:31 +14 2026 +I: pbuilder-time-stamp: 1770089491