Diff of the two buildlogs: -- --- b1/build.log 2025-10-26 05:04:49.254894554 +0000 +++ b2/build.log 2025-10-26 05:06:19.479015940 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 27 23:26:38 -12 2026 -I: pbuilder-time-stamp: 1795865198 +I: Current time: Sun Oct 26 19:04:51 +14 2025 +I: pbuilder-time-stamp: 1761455091 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-reproducible-base.tgz] I: copying local configuration @@ -27,53 +27,85 @@ 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/1197688/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/1049098/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 Oct 26 05:05 /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/1049098/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/1049098/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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(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='forky' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=forky + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='20cf3ad444044b1aa3dd7c6136799109' - 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='1197688' - PS1='# ' - PS2='> ' + INVOCATION_ID=0b1138d467cc42e0bd72fe5e51123411 + 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=1049098 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.PEigcX9I/pbuilderrc_HnBY --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PEigcX9I/b1 --logfile b1/build.log snippy_4.6.0+dfsg-5.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - 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.PEigcX9I/pbuilderrc_RPyt --distribution forky --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.PEigcX9I/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + 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 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1197688/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/1049098/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -553,7 +585,7 @@ Get: 412 http://deb.debian.org/debian forky/main arm64 snp-sites arm64 2.5.1-2+b2 [14.0 kB] Get: 413 http://deb.debian.org/debian forky/main arm64 snpeff all 5.2.f+dfsg-1 [7244 B] Get: 414 http://deb.debian.org/debian forky/main arm64 vt arm64 0.57721+ds-3+b2 [720 kB] -Fetched 318 MB in 1s (220 MB/s) +Fetched 318 MB in 1s (298 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 ... 20002 files and directories currently installed.) @@ -1915,8 +1947,8 @@ Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' -Local time is now: Sat Nov 28 11:27:22 UTC 2026. -Universal Time is now: Sat Nov 28 11:27:22 UTC 2026. +Local time is now: Sun Oct 26 05:05:39 UTC 2025. +Universal Time is now: Sun Oct 26 05:05:39 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libxcb-present0:arm64 (1.17.0-2+b1) ... @@ -2440,7 +2472,11 @@ 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/1049098/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for forky +I: user script /srv/workspace/pbuilder/1049098/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 @@ -2466,54 +2502,54 @@ [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 -[23:27:31] This is snippy 4.6.0 -[23:27:31] Written by Torsten Seemann -[23:27:31] Obtained from https://github.com/tseemann/snippy -[23:27:31] Detected operating system: linux -[23:27:31] Enabling bundled linux tools. -[23:27:31] Found bwa - /usr/bin/bwa -[23:27:31] Found bcftools - /usr/bin/bcftools -[23:27:31] Found samtools - /usr/bin/samtools -[23:27:31] Found java - /usr/bin/java -[23:27:31] Found snpEff - /usr/bin/snpEff -[23:27:31] Found samclip - /usr/bin/samclip -[23:27:31] Found seqtk - /usr/bin/seqtk -[23:27:31] Found parallel - /usr/bin/parallel -[23:27:31] Found freebayes - /usr/bin/freebayes -[23:27:31] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[23:27:31] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[23:27:31] Found vcfstreamsort - /usr/bin/vcfstreamsort -[23:27:31] Found vcfuniq - /usr/bin/vcfuniq -[23:27:31] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[23:27:31] Found gzip - /usr/bin/gzip -[23:27:31] Found vt - /usr/bin/vt -[23:27:31] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[23:27:31] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[23:27:31] Checking version: samtools --version is >= 1.7 - ok, have 1.22 -[23:27:31] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 -[23:27:31] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[23:27:31] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[23:27:31] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 -[23:27:31] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[23:27:31] Treating reference as 'fasta' format. -[23:27:31] Will use 2 CPU cores. -[23:27:31] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq -[23:27:31] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq -[23:27:31] Used --force, will overwrite existing S1 -[23:27:31] Changing working directory: S1 -[23:27:31] Creating reference folder: reference -[23:27:31] Extracting FASTA and GFF from reference. -[23:27:31] Wrote 3 sequences to ref.fa -[23:27:31] Wrote 0 features to ref.gff -[23:27:31] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[23:27:31] Using BAM RG (Read Group) ID: S1 -[23:27:31] Running: samtools faidx reference/ref.fa 2>> snps.log -[23:27:31] Running: bwa index reference/ref.fa 2>> snps.log -[23:27:31] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[23:27:31] Running: ln -sf reference/ref.fa . 2>> snps.log -[23:27:31] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[23:27:31] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[23:27:31] 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 +[19:05:56] This is snippy 4.6.0 +[19:05:56] Written by Torsten Seemann +[19:05:56] Obtained from https://github.com/tseemann/snippy +[19:05:56] Detected operating system: linux +[19:05:56] Enabling bundled linux tools. +[19:05:56] Found bwa - /usr/bin/bwa +[19:05:56] Found bcftools - /usr/bin/bcftools +[19:05:56] Found samtools - /usr/bin/samtools +[19:05:56] Found java - /usr/bin/java +[19:05:56] Found snpEff - /usr/bin/snpEff +[19:05:56] Found samclip - /usr/bin/samclip +[19:05:56] Found seqtk - /usr/bin/seqtk +[19:05:56] Found parallel - /usr/bin/parallel +[19:05:56] Found freebayes - /usr/bin/freebayes +[19:05:56] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[19:05:56] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[19:05:56] Found vcfstreamsort - /usr/bin/vcfstreamsort +[19:05:56] Found vcfuniq - /usr/bin/vcfuniq +[19:05:56] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[19:05:56] Found gzip - /usr/bin/gzip +[19:05:56] Found vt - /usr/bin/vt +[19:05:56] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[19:05:56] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[19:05:56] Checking version: samtools --version is >= 1.7 - ok, have 1.22 +[19:05:56] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 +[19:05:56] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[19:05:56] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[19:05:56] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 +[19:05:56] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[19:05:56] Treating reference as 'fasta' format. +[19:05:56] Will use 2 CPU cores. +[19:05:56] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq +[19:05:56] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq +[19:05:56] Used --force, will overwrite existing S1 +[19:05:56] Changing working directory: S1 +[19:05:56] Creating reference folder: reference +[19:05:56] Extracting FASTA and GFF from reference. +[19:05:56] Wrote 3 sequences to ref.fa +[19:05:56] Wrote 0 features to ref.gff +[19:05:56] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[19:05:56] Using BAM RG (Read Group) ID: S1 +[19:05:56] Running: samtools faidx reference/ref.fa 2>> snps.log +[19:05:56] Running: bwa index reference/ref.fa 2>> snps.log +[19:05:56] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[19:05:56] Running: ln -sf reference/ref.fa . 2>> snps.log +[19:05:56] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[19:05:56] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[19:05:56] 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) @@ -2528,17 +2564,17 @@ [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 1.189 CPU sec, 0.596 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.458 CPU sec, 0.731 real sec [main] Version: 0.7.19-r1273 [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: 0.674 sec; CPU: 1.216 sec +[main] Real time: 0.825 sec; CPU: 1.520 sec [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978 [samclip] Header contained 6 lines [samclip] Done. -[23:27:32] Running: samtools index snps.bam 2>> snps.log -[23:27:32] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[23:27:32] 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 -[23:27:33] 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 +[19:05:58] Running: samtools index snps.bam 2>> snps.log +[19:05:58] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[19:05:58] 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 +[19:05:59] 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 - @@ -2575,43 +2611,43 @@ Time elapsed: 0.01s -[23:27:34] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[23:27:34] 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 -[23:27:34] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[23:27:34] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[23:27:34] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[23:27:34] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[23:27:34] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[23:27:34] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[23:27:34] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[23:27:34] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[23:27:34] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[23:27:34] Marked 749 heterozygous sites with 'n' -[23:27:34] Creating extra output files: BED GFF CSV TXT HTML -[23:27:34] Identified 261 variants. -[23:27:34] Result folder: S1 -[23:27:34] Result files: -[23:27:34] * S1/snps.aligned.fa -[23:27:34] * S1/snps.bam -[23:27:34] * S1/snps.bam.bai -[23:27:34] * S1/snps.bed -[23:27:34] * S1/snps.consensus.fa -[23:27:34] * S1/snps.consensus.subs.fa -[23:27:34] * S1/snps.csv -[23:27:34] * S1/snps.filt.vcf -[23:27:34] * S1/snps.gff -[23:27:34] * S1/snps.html -[23:27:34] * S1/snps.log -[23:27:34] * S1/snps.raw.vcf -[23:27:34] * S1/snps.subs.vcf -[23:27:34] * S1/snps.tab -[23:27:34] * S1/snps.txt -[23:27:34] * S1/snps.vcf -[23:27:34] * S1/snps.vcf.gz -[23:27:34] * S1/snps.vcf.gz.csi -[23:27:34] Walltime used: 3 seconds -[23:27:34] Wishing you a life free of homopolymer errors. -[23:27:34] Done. +[19:05:59] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[19:05:59] 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 +[19:05:59] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[19:05:59] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[19:05:59] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[19:05:59] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[19:05:59] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[19:05:59] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[19:05:59] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[19:05:59] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[19:05:59] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[19:06:00] Marked 749 heterozygous sites with 'n' +[19:06:00] Creating extra output files: BED GFF CSV TXT HTML +[19:06:00] Identified 261 variants. +[19:06:00] Result folder: S1 +[19:06:00] Result files: +[19:06:00] * S1/snps.aligned.fa +[19:06:00] * S1/snps.bam +[19:06:00] * S1/snps.bam.bai +[19:06:00] * S1/snps.bed +[19:06:00] * S1/snps.consensus.fa +[19:06:00] * S1/snps.consensus.subs.fa +[19:06:00] * S1/snps.csv +[19:06:00] * S1/snps.filt.vcf +[19:06:00] * S1/snps.gff +[19:06:00] * S1/snps.html +[19:06:00] * S1/snps.log +[19:06:00] * S1/snps.raw.vcf +[19:06:00] * S1/snps.subs.vcf +[19:06:00] * S1/snps.tab +[19:06:00] * S1/snps.txt +[19:06:00] * S1/snps.vcf +[19:06:00] * S1/snps.vcf.gz +[19:06:00] * S1/snps.vcf.gz.csi +[19:06:00] Walltime used: 4 seconds +[19:06:00] Did you know? Snippy is a combination of SNP, Skippy, and snappy. +[19:06:00] Done. mkdir -p S2 wgsim -S 2 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2620,54 +2656,54 @@ [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 -[23:27:34] This is snippy 4.6.0 -[23:27:34] Written by Torsten Seemann -[23:27:34] Obtained from https://github.com/tseemann/snippy -[23:27:34] Detected operating system: linux -[23:27:34] Enabling bundled linux tools. -[23:27:34] Found bwa - /usr/bin/bwa -[23:27:34] Found bcftools - /usr/bin/bcftools -[23:27:34] Found samtools - /usr/bin/samtools -[23:27:34] Found java - /usr/bin/java -[23:27:34] Found snpEff - /usr/bin/snpEff -[23:27:34] Found samclip - /usr/bin/samclip -[23:27:34] Found seqtk - /usr/bin/seqtk -[23:27:34] Found parallel - /usr/bin/parallel -[23:27:34] Found freebayes - /usr/bin/freebayes -[23:27:34] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[23:27:34] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[23:27:34] Found vcfstreamsort - /usr/bin/vcfstreamsort -[23:27:34] Found vcfuniq - /usr/bin/vcfuniq -[23:27:34] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[23:27:34] Found gzip - /usr/bin/gzip -[23:27:34] Found vt - /usr/bin/vt -[23:27:34] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[23:27:34] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[23:27:34] Checking version: samtools --version is >= 1.7 - ok, have 1.22 -[23:27:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 -[23:27:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[23:27:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[23:27:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 -[23:27:34] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[23:27:34] Treating reference as 'fasta' format. -[23:27:34] Will use 2 CPU cores. -[23:27:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq -[23:27:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq -[23:27:34] Used --force, will overwrite existing S2 -[23:27:34] Changing working directory: S2 -[23:27:34] Creating reference folder: reference -[23:27:34] Extracting FASTA and GFF from reference. -[23:27:34] Wrote 3 sequences to ref.fa -[23:27:34] Wrote 0 features to ref.gff -[23:27:34] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[23:27:34] Using BAM RG (Read Group) ID: S2 -[23:27:34] Running: samtools faidx reference/ref.fa 2>> snps.log -[23:27:34] Running: bwa index reference/ref.fa 2>> snps.log -[23:27:35] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[23:27:35] Running: ln -sf reference/ref.fa . 2>> snps.log -[23:27:35] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[23:27:35] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[23:27:35] 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 +[19:06:00] This is snippy 4.6.0 +[19:06:00] Written by Torsten Seemann +[19:06:00] Obtained from https://github.com/tseemann/snippy +[19:06:00] Detected operating system: linux +[19:06:00] Enabling bundled linux tools. +[19:06:00] Found bwa - /usr/bin/bwa +[19:06:00] Found bcftools - /usr/bin/bcftools +[19:06:00] Found samtools - /usr/bin/samtools +[19:06:00] Found java - /usr/bin/java +[19:06:00] Found snpEff - /usr/bin/snpEff +[19:06:00] Found samclip - /usr/bin/samclip +[19:06:00] Found seqtk - /usr/bin/seqtk +[19:06:00] Found parallel - /usr/bin/parallel +[19:06:00] Found freebayes - /usr/bin/freebayes +[19:06:00] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[19:06:00] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[19:06:00] Found vcfstreamsort - /usr/bin/vcfstreamsort +[19:06:00] Found vcfuniq - /usr/bin/vcfuniq +[19:06:00] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[19:06:00] Found gzip - /usr/bin/gzip +[19:06:00] Found vt - /usr/bin/vt +[19:06:00] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[19:06:00] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[19:06:00] Checking version: samtools --version is >= 1.7 - ok, have 1.22 +[19:06:00] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 +[19:06:00] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[19:06:00] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[19:06:00] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 +[19:06:00] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[19:06:00] Treating reference as 'fasta' format. +[19:06:00] Will use 2 CPU cores. +[19:06:00] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq +[19:06:00] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq +[19:06:00] Used --force, will overwrite existing S2 +[19:06:00] Changing working directory: S2 +[19:06:00] Creating reference folder: reference +[19:06:00] Extracting FASTA and GFF from reference. +[19:06:00] Wrote 3 sequences to ref.fa +[19:06:00] Wrote 0 features to ref.gff +[19:06:00] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[19:06:00] Using BAM RG (Read Group) ID: S2 +[19:06:00] Running: samtools faidx reference/ref.fa 2>> snps.log +[19:06:00] Running: bwa index reference/ref.fa 2>> snps.log +[19:06:00] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[19:06:00] Running: ln -sf reference/ref.fa . 2>> snps.log +[19:06:00] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[19:06:00] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[19:06:00] 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) @@ -2682,17 +2718,17 @@ [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 1.181 CPU sec, 0.704 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.469 CPU sec, 0.738 real sec [main] Version: 0.7.19-r1273 [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: 1.210 sec +[main] Real time: 0.889 sec; CPU: 1.533 sec [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987 [samclip] Header contained 6 lines [samclip] Done. -[23:27:36] Running: samtools index snps.bam 2>> snps.log -[23:27:36] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[23:27:36] 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 -[23:27:37] 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 +[19:06:02] Running: samtools index snps.bam 2>> snps.log +[19:06:02] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[19:06:02] 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 +[19:06:03] 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 - @@ -2727,45 +2763,45 @@ total no. variants observed : 246 total no. reference observed : 0 -Time elapsed: 0.00s +Time elapsed: 0.01s -[23:27:37] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[23:27:37] 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 -[23:27:37] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[23:27:37] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[23:27:37] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[23:27:37] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[23:27:37] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[23:27:37] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[23:27:37] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[23:27:37] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[23:27:37] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[23:27:37] Marked 841 heterozygous sites with 'n' -[23:27:37] Creating extra output files: BED GFF CSV TXT HTML -[23:27:37] Identified 246 variants. -[23:27:37] Result folder: S2 -[23:27:37] Result files: -[23:27:37] * S2/snps.aligned.fa -[23:27:37] * S2/snps.bam -[23:27:37] * S2/snps.bam.bai -[23:27:37] * S2/snps.bed -[23:27:37] * S2/snps.consensus.fa -[23:27:37] * S2/snps.consensus.subs.fa -[23:27:37] * S2/snps.csv -[23:27:37] * S2/snps.filt.vcf -[23:27:37] * S2/snps.gff -[23:27:37] * S2/snps.html -[23:27:37] * S2/snps.log -[23:27:37] * S2/snps.raw.vcf -[23:27:37] * S2/snps.subs.vcf -[23:27:37] * S2/snps.tab -[23:27:37] * S2/snps.txt -[23:27:37] * S2/snps.vcf -[23:27:37] * S2/snps.vcf.gz -[23:27:37] * S2/snps.vcf.gz.csi -[23:27:37] Walltime used: 3 seconds -[23:27:37] Found a bug? Post it at https://github.com/tseemann/snippy/issues -[23:27:37] Done. +[19:06:03] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[19:06:03] 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 +[19:06:03] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[19:06:03] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[19:06:03] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[19:06:03] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[19:06:03] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[19:06:03] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[19:06:04] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[19:06:04] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[19:06:04] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[19:06:04] Marked 841 heterozygous sites with 'n' +[19:06:04] Creating extra output files: BED GFF CSV TXT HTML +[19:06:04] Identified 246 variants. +[19:06:04] Result folder: S2 +[19:06:04] Result files: +[19:06:04] * S2/snps.aligned.fa +[19:06:04] * S2/snps.bam +[19:06:04] * S2/snps.bam.bai +[19:06:04] * S2/snps.bed +[19:06:04] * S2/snps.consensus.fa +[19:06:04] * S2/snps.consensus.subs.fa +[19:06:04] * S2/snps.csv +[19:06:04] * S2/snps.filt.vcf +[19:06:04] * S2/snps.gff +[19:06:04] * S2/snps.html +[19:06:04] * S2/snps.log +[19:06:04] * S2/snps.raw.vcf +[19:06:04] * S2/snps.subs.vcf +[19:06:04] * S2/snps.tab +[19:06:04] * S2/snps.txt +[19:06:04] * S2/snps.vcf +[19:06:04] * S2/snps.vcf.gz +[19:06:04] * S2/snps.vcf.gz.csi +[19:06:04] Walltime used: 4 seconds +[19:06:04] The Snippy manual is at https://github.com/tseemann/snippy/blob/master/README.md +[19:06:04] Done. mkdir -p S3 wgsim -S 3 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2774,59 +2810,59 @@ [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 -[23:27:38] This is snippy 4.6.0 -[23:27:38] Written by Torsten Seemann -[23:27:38] Obtained from https://github.com/tseemann/snippy -[23:27:38] Detected operating system: linux -[23:27:38] Enabling bundled linux tools. -[23:27:38] Found bwa - /usr/bin/bwa -[23:27:38] Found bcftools - /usr/bin/bcftools -[23:27:38] Found samtools - /usr/bin/samtools -[23:27:38] Found java - /usr/bin/java -[23:27:38] Found snpEff - /usr/bin/snpEff -[23:27:38] Found samclip - /usr/bin/samclip -[23:27:38] Found seqtk - /usr/bin/seqtk -[23:27:38] Found parallel - /usr/bin/parallel -[23:27:38] Found freebayes - /usr/bin/freebayes -[23:27:38] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[23:27:38] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[23:27:38] Found vcfstreamsort - /usr/bin/vcfstreamsort -[23:27:38] Found vcfuniq - /usr/bin/vcfuniq -[23:27:38] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[23:27:38] Found gzip - /usr/bin/gzip -[23:27:38] Found vt - /usr/bin/vt -[23:27:38] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[23:27:38] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[23:27:38] Checking version: samtools --version is >= 1.7 - ok, have 1.22 -[23:27:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 -[23:27:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[23:27:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[23:27:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 -[23:27:38] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[23:27:38] Treating reference as 'fasta' format. -[23:27:38] Will use 2 CPU cores. -[23:27:38] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq -[23:27:38] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq -[23:27:38] Used --force, will overwrite existing S3 -[23:27:38] Changing working directory: S3 -[23:27:38] Creating reference folder: reference -[23:27:38] Extracting FASTA and GFF from reference. -[23:27:38] Wrote 3 sequences to ref.fa -[23:27:38] Wrote 0 features to ref.gff -[23:27:38] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[23:27:38] Using BAM RG (Read Group) ID: S3 -[23:27:38] Running: samtools faidx reference/ref.fa 2>> snps.log -[23:27:38] Running: bwa index reference/ref.fa 2>> snps.log -[23:27:38] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[23:27:38] Running: ln -sf reference/ref.fa . 2>> snps.log -[23:27:38] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[23:27:38] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[23:27:38] 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 +[19:06:04] This is snippy 4.6.0 +[19:06:04] Written by Torsten Seemann +[19:06:04] Obtained from https://github.com/tseemann/snippy +[19:06:04] Detected operating system: linux +[19:06:04] Enabling bundled linux tools. +[19:06:04] Found bwa - /usr/bin/bwa +[19:06:04] Found bcftools - /usr/bin/bcftools +[19:06:04] Found samtools - /usr/bin/samtools +[19:06:04] Found java - /usr/bin/java +[19:06:04] Found snpEff - /usr/bin/snpEff +[19:06:04] Found samclip - /usr/bin/samclip +[19:06:04] Found seqtk - /usr/bin/seqtk +[19:06:04] Found parallel - /usr/bin/parallel +[19:06:04] Found freebayes - /usr/bin/freebayes +[19:06:04] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[19:06:04] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[19:06:04] Found vcfstreamsort - /usr/bin/vcfstreamsort +[19:06:04] Found vcfuniq - /usr/bin/vcfuniq +[19:06:04] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[19:06:04] Found gzip - /usr/bin/gzip +[19:06:04] Found vt - /usr/bin/vt +[19:06:04] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[19:06:04] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[19:06:04] Checking version: samtools --version is >= 1.7 - ok, have 1.22 +[19:06:04] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 +[19:06:04] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[19:06:04] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[19:06:04] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 +[19:06:04] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[19:06:04] Treating reference as 'fasta' format. +[19:06:04] Will use 2 CPU cores. +[19:06:04] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq +[19:06:04] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq +[19:06:04] Used --force, will overwrite existing S3 +[19:06:04] Changing working directory: S3 +[19:06:04] Creating reference folder: reference +[19:06:04] Extracting FASTA and GFF from reference. +[19:06:05] Wrote 3 sequences to ref.fa +[19:06:05] Wrote 0 features to ref.gff +[19:06:05] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[19:06:05] Using BAM RG (Read Group) ID: S3 +[19:06:05] Running: samtools faidx reference/ref.fa 2>> snps.log +[19:06:05] Running: bwa index reference/ref.fa 2>> snps.log +[19:06:05] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[19:06:05] Running: ln -sf reference/ref.fa . 2>> snps.log +[19:06:05] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[19:06:05] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[19:06:05] 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... @@ -2836,17 +2872,17 @@ [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 1.196 CPU sec, 0.619 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.486 CPU sec, 0.746 real sec [main] Version: 0.7.19-r1273 [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: 0.725 sec; CPU: 1.224 sec +[main] Real time: 0.897 sec; CPU: 1.547 sec [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970 [samclip] Header contained 6 lines [samclip] Done. -[23:27:39] Running: samtools index snps.bam 2>> snps.log -[23:27:39] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[23:27:39] 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 -[23:27:40] 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 +[19:06:06] Running: samtools index snps.bam 2>> snps.log +[19:06:06] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[19:06:06] 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 +[19:06:07] 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 - @@ -2881,45 +2917,45 @@ total no. variants observed : 254 total no. reference observed : 0 -Time elapsed: 0.00s +Time elapsed: 0.01s -[23:27:40] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[23:27:40] 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 -[23:27:40] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[23:27:40] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[23:27:40] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[23:27:40] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[23:27:40] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[23:27:40] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[23:27:40] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[23:27:40] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[23:27:40] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[23:27:40] Marked 846 heterozygous sites with 'n' -[23:27:40] Creating extra output files: BED GFF CSV TXT HTML -[23:27:40] Identified 254 variants. -[23:27:40] Result folder: S3 -[23:27:40] Result files: -[23:27:40] * S3/snps.aligned.fa -[23:27:40] * S3/snps.bam -[23:27:40] * S3/snps.bam.bai -[23:27:40] * S3/snps.bed -[23:27:40] * S3/snps.consensus.fa -[23:27:40] * S3/snps.consensus.subs.fa -[23:27:40] * S3/snps.csv -[23:27:40] * S3/snps.filt.vcf -[23:27:40] * S3/snps.gff -[23:27:40] * S3/snps.html -[23:27:40] * S3/snps.log -[23:27:40] * S3/snps.raw.vcf -[23:27:40] * S3/snps.subs.vcf -[23:27:40] * S3/snps.tab -[23:27:40] * S3/snps.txt -[23:27:40] * S3/snps.vcf -[23:27:40] * S3/snps.vcf.gz -[23:27:40] * S3/snps.vcf.gz.csi -[23:27:40] Walltime used: 2 seconds -[23:27:40] Wishing you a life free of homopolymer errors. -[23:27:40] Done. +[19:06:07] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[19:06:07] 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 +[19:06:08] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[19:06:08] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[19:06:08] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[19:06:08] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[19:06:08] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[19:06:08] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[19:06:08] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[19:06:08] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[19:06:08] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[19:06:08] Marked 846 heterozygous sites with 'n' +[19:06:08] Creating extra output files: BED GFF CSV TXT HTML +[19:06:08] Identified 254 variants. +[19:06:08] Result folder: S3 +[19:06:08] Result files: +[19:06:08] * S3/snps.aligned.fa +[19:06:08] * S3/snps.bam +[19:06:08] * S3/snps.bam.bai +[19:06:08] * S3/snps.bed +[19:06:08] * S3/snps.consensus.fa +[19:06:08] * S3/snps.consensus.subs.fa +[19:06:08] * S3/snps.csv +[19:06:08] * S3/snps.filt.vcf +[19:06:08] * S3/snps.gff +[19:06:08] * S3/snps.html +[19:06:08] * S3/snps.log +[19:06:08] * S3/snps.raw.vcf +[19:06:08] * S3/snps.subs.vcf +[19:06:08] * S3/snps.tab +[19:06:08] * S3/snps.txt +[19:06:08] * S3/snps.vcf +[19:06:08] * S3/snps.vcf.gz +[19:06:08] * S3/snps.vcf.gz.csi +[19:06:08] Walltime used: 4 seconds +[19:06:08] Found a bug? Post it at https://github.com/tseemann/snippy/issues +[19:06:08] Done. mkdir -p S4 wgsim -S 4 \ -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \ @@ -2928,54 +2964,54 @@ [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 -[23:27:41] This is snippy 4.6.0 -[23:27:41] Written by Torsten Seemann -[23:27:41] Obtained from https://github.com/tseemann/snippy -[23:27:41] Detected operating system: linux -[23:27:41] Enabling bundled linux tools. -[23:27:41] Found bwa - /usr/bin/bwa -[23:27:41] Found bcftools - /usr/bin/bcftools -[23:27:41] Found samtools - /usr/bin/samtools -[23:27:41] Found java - /usr/bin/java -[23:27:41] Found snpEff - /usr/bin/snpEff -[23:27:41] Found samclip - /usr/bin/samclip -[23:27:41] Found seqtk - /usr/bin/seqtk -[23:27:41] Found parallel - /usr/bin/parallel -[23:27:41] Found freebayes - /usr/bin/freebayes -[23:27:41] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel -[23:27:41] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py -[23:27:41] Found vcfstreamsort - /usr/bin/vcfstreamsort -[23:27:41] Found vcfuniq - /usr/bin/vcfuniq -[23:27:41] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader -[23:27:41] Found gzip - /usr/bin/gzip -[23:27:41] Found vt - /usr/bin/vt -[23:27:41] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab -[23:27:41] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report -[23:27:41] Checking version: samtools --version is >= 1.7 - ok, have 1.22 -[23:27:41] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 -[23:27:41] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 -[23:27:41] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 -[23:27:41] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 -[23:27:41] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna -[23:27:41] Treating reference as 'fasta' format. -[23:27:41] Will use 2 CPU cores. -[23:27:41] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq -[23:27:41] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq -[23:27:41] Used --force, will overwrite existing S4 -[23:27:41] Changing working directory: S4 -[23:27:41] Creating reference folder: reference -[23:27:41] Extracting FASTA and GFF from reference. -[23:27:41] Wrote 3 sequences to ref.fa -[23:27:41] Wrote 0 features to ref.gff -[23:27:41] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. -[23:27:41] Using BAM RG (Read Group) ID: S4 -[23:27:41] Running: samtools faidx reference/ref.fa 2>> snps.log -[23:27:41] Running: bwa index reference/ref.fa 2>> snps.log -[23:27:41] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log -[23:27:41] Running: ln -sf reference/ref.fa . 2>> snps.log -[23:27:41] Running: ln -sf reference/ref.fa.fai . 2>> snps.log -[23:27:41] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log -[23:27:41] 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 +[19:06:08] This is snippy 4.6.0 +[19:06:08] Written by Torsten Seemann +[19:06:08] Obtained from https://github.com/tseemann/snippy +[19:06:08] Detected operating system: linux +[19:06:08] Enabling bundled linux tools. +[19:06:08] Found bwa - /usr/bin/bwa +[19:06:08] Found bcftools - /usr/bin/bcftools +[19:06:08] Found samtools - /usr/bin/samtools +[19:06:08] Found java - /usr/bin/java +[19:06:08] Found snpEff - /usr/bin/snpEff +[19:06:08] Found samclip - /usr/bin/samclip +[19:06:08] Found seqtk - /usr/bin/seqtk +[19:06:08] Found parallel - /usr/bin/parallel +[19:06:08] Found freebayes - /usr/bin/freebayes +[19:06:08] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel +[19:06:08] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py +[19:06:08] Found vcfstreamsort - /usr/bin/vcfstreamsort +[19:06:08] Found vcfuniq - /usr/bin/vcfuniq +[19:06:08] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader +[19:06:08] Found gzip - /usr/bin/gzip +[19:06:08] Found vt - /usr/bin/vt +[19:06:08] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab +[19:06:08] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report +[19:06:09] Checking version: samtools --version is >= 1.7 - ok, have 1.22 +[19:06:09] Checking version: bcftools --version is >= 1.7 - ok, have 1.22 +[19:06:09] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8 +[19:06:09] Checking version: snpEff -version is >= 4.3 - ok, have 5.2 +[19:06:09] Checking version: bwa is >= 0.7.12 - ok, have 0.7.19 +[19:06:09] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna +[19:06:09] Treating reference as 'fasta' format. +[19:06:09] Will use 2 CPU cores. +[19:06:09] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq +[19:06:09] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq +[19:06:09] Used --force, will overwrite existing S4 +[19:06:09] Changing working directory: S4 +[19:06:09] Creating reference folder: reference +[19:06:09] Extracting FASTA and GFF from reference. +[19:06:09] Wrote 3 sequences to ref.fa +[19:06:09] Wrote 0 features to ref.gff +[19:06:09] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time. +[19:06:09] Using BAM RG (Read Group) ID: S4 +[19:06:09] Running: samtools faidx reference/ref.fa 2>> snps.log +[19:06:09] Running: bwa index reference/ref.fa 2>> snps.log +[19:06:09] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log +[19:06:09] Running: ln -sf reference/ref.fa . 2>> snps.log +[19:06:09] Running: ln -sf reference/ref.fa.fai . 2>> snps.log +[19:06:09] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log +[19:06:09] 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) @@ -2990,17 +3026,17 @@ [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 1.257 CPU sec, 0.631 real sec +[M::mem_process_seqs] Processed 24000 reads in 1.450 CPU sec, 0.727 real sec [main] Version: 0.7.19-r1273 [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: 0.707 sec; CPU: 1.295 sec +[main] Real time: 0.878 sec; CPU: 1.514 sec [samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974 [samclip] Header contained 6 lines [samclip] Done. -[23:27:42] Running: samtools index snps.bam 2>> snps.log -[23:27:42] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log -[23:27:42] 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 -[23:27:43] 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 +[19:06:10] Running: samtools index snps.bam 2>> snps.log +[19:06:10] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log +[19:06:10] 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 +[19:06:12] 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 - @@ -3035,45 +3071,45 @@ total no. variants observed : 257 total no. reference observed : 0 -Time elapsed: 0.00s +Time elapsed: 0.01s -[23:27:43] Running: cp snps.filt.vcf snps.vcf 2>> snps.log -[23:27:43] 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 -[23:27:43] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log -[23:27:43] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log -[23:27:43] Running: bcftools index -f snps.vcf.gz 2>> snps.log -[23:27:43] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log -[23:27:43] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log -[23:27:43] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log -[23:27:43] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log -[23:27:43] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log -[23:27:43] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa -[23:27:44] Marked 799 heterozygous sites with 'n' -[23:27:44] Creating extra output files: BED GFF CSV TXT HTML -[23:27:44] Identified 257 variants. -[23:27:44] Result folder: S4 -[23:27:44] Result files: -[23:27:44] * S4/snps.aligned.fa -[23:27:44] * S4/snps.bam -[23:27:44] * S4/snps.bam.bai -[23:27:44] * S4/snps.bed -[23:27:44] * S4/snps.consensus.fa -[23:27:44] * S4/snps.consensus.subs.fa -[23:27:44] * S4/snps.csv -[23:27:44] * S4/snps.filt.vcf -[23:27:44] * S4/snps.gff -[23:27:44] * S4/snps.html -[23:27:44] * S4/snps.log -[23:27:44] * S4/snps.raw.vcf -[23:27:44] * S4/snps.subs.vcf -[23:27:44] * S4/snps.tab -[23:27:44] * S4/snps.txt -[23:27:44] * S4/snps.vcf -[23:27:44] * S4/snps.vcf.gz -[23:27:44] * S4/snps.vcf.gz.csi -[23:27:44] Walltime used: 3 seconds -[23:27:44] May the SNPs be with you. -[23:27:44] Done. +[19:06:12] Running: cp snps.filt.vcf snps.vcf 2>> snps.log +[19:06:12] 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 +[19:06:12] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log +[19:06:12] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log +[19:06:12] Running: bcftools index -f snps.vcf.gz 2>> snps.log +[19:06:12] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log +[19:06:12] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log +[19:06:12] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log +[19:06:12] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log +[19:06:12] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log +[19:06:12] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa +[19:06:12] Marked 799 heterozygous sites with 'n' +[19:06:12] Creating extra output files: BED GFF CSV TXT HTML +[19:06:12] Identified 257 variants. +[19:06:12] Result folder: S4 +[19:06:12] Result files: +[19:06:12] * S4/snps.aligned.fa +[19:06:12] * S4/snps.bam +[19:06:12] * S4/snps.bam.bai +[19:06:12] * S4/snps.bed +[19:06:12] * S4/snps.consensus.fa +[19:06:12] * S4/snps.consensus.subs.fa +[19:06:12] * S4/snps.csv +[19:06:12] * S4/snps.filt.vcf +[19:06:12] * S4/snps.gff +[19:06:12] * S4/snps.html +[19:06:12] * S4/snps.log +[19:06:12] * S4/snps.raw.vcf +[19:06:12] * S4/snps.subs.vcf +[19:06:12] * S4/snps.tab +[19:06:12] * S4/snps.txt +[19:06:12] * S4/snps.vcf +[19:06:12] * S4/snps.vcf.gz +[19:06:12] * S4/snps.vcf.gz.csi +[19:06:12] Walltime used: 4 seconds +[19:06:12] May the SNPs be with you. +[19:06:12] 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 @@ -3106,7 +3142,7 @@ Generating core.full.aln Creating TSV file: core.txt Running: snp-sites -c -o core.aln core.full.aln -This analysis is totally hard-core! +Have a suggestion? Tell me at http://github.com/tseemann/snippy/issues Done. This is snippy-core 4.6.0 Obtained from http://github.com/tseemann/snippy @@ -3140,7 +3176,7 @@ Generating core-mask.full.aln Creating TSV file: core-mask.txt Running: snp-sites -c -o core-mask.aln core-mask.full.aln -Run 'snp-sites -b -c -o phylo.aln core.full.aln' for IQTree, BEAST, RaxML +This analysis is totally hard-core! Done. wc -l S?/snps.tab 262 S1/snps.tab @@ -3178,12 +3214,14 @@ 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/1049098/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/1049098/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/1197688 and its subdirectories -I: Current time: Fri Nov 27 23:27:47 -12 2026 -I: pbuilder-time-stamp: 1795865267 +I: removing directory /srv/workspace/pbuilder/1049098 and its subdirectories +I: Current time: Sun Oct 26 19:06:18 +14 2025 +I: pbuilder-time-stamp: 1761455178