Diff of the two buildlogs:

--
--- b1/build.log	2025-02-22 00:15:12.672271718 +0000
+++ b2/build.log	2025-02-22 00:16:49.187883008 +0000
@@ -1,6 +1,6 @@
 I: pbuilder: network access will be disabled during build
-I: Current time: Thu Mar 26 18:33:54 -12 2026
-I: pbuilder-time-stamp: 1774593234
+I: Current time: Sat Feb 22 14:15:15 +14 2025
+I: pbuilder-time-stamp: 1740183315
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz]
 I: copying local configuration
@@ -27,52 +27,84 @@
 dpkg-source: info: applying make-4.4.1.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/1272158/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/671649/tmp/hooks/D01_modify_environment starting
+debug: Running on codethink04-arm64.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Feb 22 00:15 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/671649/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/671649/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build/reproducible-path'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='arm64'
-  DEBIAN_FRONTEND='noninteractive'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu")
+  BASH_VERSION='5.2.37(1)-release'
+  BUILDDIR=/build/reproducible-path
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=arm64
+  DEBIAN_FRONTEND=noninteractive
   DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 '
-  DISTRIBUTION='trixie'
-  HOME='/root'
-  HOST_ARCH='arm64'
+  DIRSTACK=()
+  DISTRIBUTION=trixie
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=aarch64
+  HOST_ARCH=arm64
   IFS=' 	
   '
-  INVOCATION_ID='308a4e9ee74c445286fdee80d0e2ecf2'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='1272158'
-  PS1='# '
-  PS2='> '
+  INVOCATION_ID=12b53ee092914f6c9077280e15654abf
+  LANG=C
+  LANGUAGE=nl_BE:nl
+  LC_ALL=C
+  MACHTYPE=aarch64-unknown-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=671649
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.pzeb5dlB/pbuilderrc_owMa --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pzeb5dlB/b1 --logfile b1/build.log snippy_4.6.0+dfsg-5.dsc'
-  SUDO_GID='109'
-  SUDO_UID='104'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://192.168.101.4:3128'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.pzeb5dlB/pbuilderrc_03bD --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.pzeb5dlB/b2 --logfile b2/build.log snippy_4.6.0+dfsg-5.dsc'
+  SUDO_GID=109
+  SUDO_UID=104
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://192.168.101.4:3128
 I: uname -a
-  Linux codethink03-arm64 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-31-cloud-arm64 #1 SMP Debian 6.1.128-1 (2025-02-07) aarch64 GNU/Linux
 I: ls -l /bin
-  lrwxrwxrwx 1 root root 7 Nov 22  2024 /bin -> usr/bin
-I: user script /srv/workspace/pbuilder/1272158/tmp/hooks/D02_print_environment finished
+  lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin
+I: user script /srv/workspace/pbuilder/671649/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -554,7 +586,7 @@
 Get: 414 http://deb.debian.org/debian trixie/main arm64 snp-sites arm64 2.5.1-2+b2 [14.0 kB]
 Get: 415 http://deb.debian.org/debian trixie/main arm64 snpeff all 5.2.f+dfsg-1 [7244 B]
 Get: 416 http://deb.debian.org/debian trixie/main arm64 vt arm64 0.57721+ds-3+b2 [720 kB]
-Fetched 314 MB in 4s (88.4 MB/s)
+Fetched 314 MB in 1s (253 MB/s)
 Preconfiguring packages ...
 Selecting previously unselected package libsystemd-shared:arm64.
 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19923 files and directories currently installed.)
@@ -1922,8 +1954,8 @@
 Setting up tzdata (2025a-2) ...
 
 Current default time zone: 'Etc/UTC'
-Local time is now:      Fri Mar 27 06:36:16 UTC 2026.
-Universal Time is now:  Fri Mar 27 06:36:16 UTC 2026.
+Local time is now:      Sat Feb 22 00:16:06 UTC 2025.
+Universal Time is now:  Sat Feb 22 00:16:06 UTC 2025.
 Run 'dpkg-reconfigure tzdata' if you wish to change it.
 
 Setting up libxcb-present0:arm64 (1.17.0-2+b1) ...
@@ -2450,7 +2482,11 @@
 Building tag database...
  -> Finished parsing the build-deps
 I: Building the package
-I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../snippy_4.6.0+dfsg-5_source.changes
+I: user script /srv/workspace/pbuilder/671649/tmp/hooks/A99_set_merged_usr starting
+Not re-configuring usrmerge for trixie
+I: user script /srv/workspace/pbuilder/671649/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/reproducible-path/snippy-4.6.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../snippy_4.6.0+dfsg-5_source.changes
 dpkg-buildpackage: info: source package snippy
 dpkg-buildpackage: info: source version 4.6.0+dfsg-5
 dpkg-buildpackage: info: source distribution unstable
@@ -2476,54 +2512,54 @@
 [wgsim_core] calculating the total length of the reference sequence...
 [wgsim_core] 3 sequences, total length: 317336
 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S1 --R1 S1/R1.fq --R2 S1/R2.fq
-[18:37:21] This is snippy 4.6.0
-[18:37:21] Written by Torsten Seemann
-[18:37:21] Obtained from https://github.com/tseemann/snippy
-[18:37:21] Detected operating system: linux
-[18:37:21] Enabling bundled linux tools.
-[18:37:21] Found bwa - /usr/bin/bwa
-[18:37:21] Found bcftools - /usr/bin/bcftools
-[18:37:21] Found samtools - /usr/bin/samtools
-[18:37:21] Found java - /usr/bin/java
-[18:37:21] Found snpEff - /usr/bin/snpEff
-[18:37:21] Found samclip - /usr/bin/samclip
-[18:37:21] Found seqtk - /usr/bin/seqtk
-[18:37:21] Found parallel - /usr/bin/parallel
-[18:37:21] Found freebayes - /usr/bin/freebayes
-[18:37:21] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
-[18:37:21] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
-[18:37:21] Found vcfstreamsort - /usr/bin/vcfstreamsort
-[18:37:21] Found vcfuniq - /usr/bin/vcfuniq
-[18:37:21] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
-[18:37:21] Found gzip - /usr/bin/gzip
-[18:37:21] Found vt - /usr/bin/vt
-[18:37:21] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
-[18:37:22] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
-[18:37:22] Checking version: samtools --version is >= 1.7 - ok, have 1.21
-[18:37:22] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
-[18:37:22] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
-[18:37:22] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
-[18:37:22] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
-[18:37:22] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
-[18:37:22] Treating reference as 'fasta' format.
-[18:37:22] Will use 2 CPU cores.
-[18:37:22] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq
-[18:37:22] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq
-[18:37:22] Used --force, will overwrite existing S1
-[18:37:22] Changing working directory: S1
-[18:37:22] Creating reference folder: reference
-[18:37:22] Extracting FASTA and GFF from reference.
-[18:37:22] Wrote 3 sequences to ref.fa
-[18:37:22] Wrote 0 features to ref.gff
-[18:37:22] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
-[18:37:22] Using BAM RG (Read Group) ID: S1
-[18:37:22] Running: samtools faidx reference/ref.fa 2>> snps.log
-[18:37:22] Running: bwa index reference/ref.fa 2>> snps.log
-[18:37:23] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
-[18:37:23] Running: ln -sf reference/ref.fa . 2>> snps.log
-[18:37:23] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
-[18:37:23] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
-[18:37:23] Running: bwa mem  -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
+[14:16:25] This is snippy 4.6.0
+[14:16:25] Written by Torsten Seemann
+[14:16:25] Obtained from https://github.com/tseemann/snippy
+[14:16:25] Detected operating system: linux
+[14:16:25] Enabling bundled linux tools.
+[14:16:25] Found bwa - /usr/bin/bwa
+[14:16:25] Found bcftools - /usr/bin/bcftools
+[14:16:25] Found samtools - /usr/bin/samtools
+[14:16:25] Found java - /usr/bin/java
+[14:16:25] Found snpEff - /usr/bin/snpEff
+[14:16:25] Found samclip - /usr/bin/samclip
+[14:16:25] Found seqtk - /usr/bin/seqtk
+[14:16:25] Found parallel - /usr/bin/parallel
+[14:16:25] Found freebayes - /usr/bin/freebayes
+[14:16:25] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
+[14:16:25] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
+[14:16:25] Found vcfstreamsort - /usr/bin/vcfstreamsort
+[14:16:25] Found vcfuniq - /usr/bin/vcfuniq
+[14:16:25] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
+[14:16:25] Found gzip - /usr/bin/gzip
+[14:16:25] Found vt - /usr/bin/vt
+[14:16:25] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
+[14:16:25] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
+[14:16:25] Checking version: samtools --version is >= 1.7 - ok, have 1.21
+[14:16:25] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
+[14:16:25] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
+[14:16:25] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
+[14:16:25] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
+[14:16:25] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
+[14:16:25] Treating reference as 'fasta' format.
+[14:16:25] Will use 2 CPU cores.
+[14:16:25] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq
+[14:16:25] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq
+[14:16:25] Used --force, will overwrite existing S1
+[14:16:25] Changing working directory: S1
+[14:16:25] Creating reference folder: reference
+[14:16:25] Extracting FASTA and GFF from reference.
+[14:16:25] Wrote 3 sequences to ref.fa
+[14:16:25] Wrote 0 features to ref.gff
+[14:16:25] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
+[14:16:25] Using BAM RG (Read Group) ID: S1
+[14:16:25] Running: samtools faidx reference/ref.fa 2>> snps.log
+[14:16:25] Running: bwa index reference/ref.fa 2>> snps.log
+[14:16:26] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
+[14:16:26] Running: ln -sf reference/ref.fa . 2>> snps.log
+[14:16:26] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
+[14:16:26] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
+[14:16:26] Running: bwa mem  -Y -M -R '@RG\tID:S1\tSM:S1' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
 [M::bwa_idx_load_from_disk] read 0 ALT contigs
 [M::process] read 24000 sequences (2400000 bp)...
 [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
@@ -2538,17 +2574,17 @@
 [M::mem_pestat] low and high boundaries for proper pairs: (1, 437)
 [M::mem_pestat] skip orientation RF as there are not enough pairs
 [M::mem_pestat] skip orientation RR as there are not enough pairs
-[M::mem_process_seqs] Processed 24000 reads in 1.309 CPU sec, 2.555 real sec
+[M::mem_process_seqs] Processed 24000 reads in 1.373 CPU sec, 0.689 real sec
 [main] Version: 0.7.18-r1243-dirty
 [main] CMD: bwa mem -Y -M -R @RG\tID:S1\tSM:S1 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S1/R2.fq
-[main] Real time: 2.840 sec; CPU: 1.336 sec
+[main] Real time: 0.845 sec; CPU: 1.442 sec
 [samclip] Total SAM records 24000, removed 22, allowed 387, passed 23978
 [samclip] Header contained 6 lines
 [samclip] Done.
-[18:37:27] Running: samtools index snps.bam 2>> snps.log
-[18:37:27] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
-[18:37:27] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
-[18:37:30] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
+[14:16:27] Running: samtools index snps.bam 2>> snps.log
+[14:16:27] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
+[14:16:27] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
+[14:16:28] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
 normalize v0.5
 
 options:     input VCF file                                  -
@@ -2585,43 +2621,43 @@
 
 Time elapsed: 0.01s
 
-[18:37:30] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
-[18:37:30] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
-[18:37:31] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
-[18:37:31] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
-[18:37:31] Running: bcftools index -f snps.vcf.gz 2>> snps.log
-[18:37:31] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
-[18:37:31] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
-[18:37:31] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
-[18:37:31] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
-[18:37:31] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
-[18:37:31] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
-[18:37:32] Marked 749 heterozygous sites with 'n'
-[18:37:32] Creating extra output files: BED GFF CSV TXT HTML
-[18:37:32] Identified 261 variants.
-[18:37:32] Result folder: S1
-[18:37:32] Result files:
-[18:37:32] * S1/snps.aligned.fa
-[18:37:32] * S1/snps.bam
-[18:37:32] * S1/snps.bam.bai
-[18:37:32] * S1/snps.bed
-[18:37:32] * S1/snps.consensus.fa
-[18:37:32] * S1/snps.consensus.subs.fa
-[18:37:32] * S1/snps.csv
-[18:37:32] * S1/snps.filt.vcf
-[18:37:32] * S1/snps.gff
-[18:37:32] * S1/snps.html
-[18:37:32] * S1/snps.log
-[18:37:32] * S1/snps.raw.vcf
-[18:37:32] * S1/snps.subs.vcf
-[18:37:32] * S1/snps.tab
-[18:37:32] * S1/snps.txt
-[18:37:32] * S1/snps.vcf
-[18:37:32] * S1/snps.vcf.gz
-[18:37:32] * S1/snps.vcf.gz.csi
-[18:37:32] Walltime used: 11 seconds
-[18:37:32] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues
-[18:37:32] Done.
+[14:16:28] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
+[14:16:28] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
+[14:16:29] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
+[14:16:29] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
+[14:16:29] Running: bcftools index -f snps.vcf.gz 2>> snps.log
+[14:16:29] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
+[14:16:29] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
+[14:16:29] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
+[14:16:29] Running: bcftools consensus --sample S1 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
+[14:16:29] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
+[14:16:29] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
+[14:16:29] Marked 749 heterozygous sites with 'n'
+[14:16:29] Creating extra output files: BED GFF CSV TXT HTML
+[14:16:29] Identified 261 variants.
+[14:16:29] Result folder: S1
+[14:16:29] Result files:
+[14:16:29] * S1/snps.aligned.fa
+[14:16:29] * S1/snps.bam
+[14:16:29] * S1/snps.bam.bai
+[14:16:29] * S1/snps.bed
+[14:16:29] * S1/snps.consensus.fa
+[14:16:29] * S1/snps.consensus.subs.fa
+[14:16:29] * S1/snps.csv
+[14:16:29] * S1/snps.filt.vcf
+[14:16:29] * S1/snps.gff
+[14:16:29] * S1/snps.html
+[14:16:29] * S1/snps.log
+[14:16:29] * S1/snps.raw.vcf
+[14:16:29] * S1/snps.subs.vcf
+[14:16:29] * S1/snps.tab
+[14:16:29] * S1/snps.txt
+[14:16:29] * S1/snps.vcf
+[14:16:29] * S1/snps.vcf.gz
+[14:16:29] * S1/snps.vcf.gz.csi
+[14:16:29] Walltime used: 4 seconds
+[14:16:29] Did you know? Snippy is a combination of SNP, Skippy, and snappy.
+[14:16:29] Done.
 mkdir -p S2
 wgsim -S 2 \
          -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
@@ -2630,59 +2666,59 @@
 [wgsim_core] calculating the total length of the reference sequence...
 [wgsim_core] 3 sequences, total length: 317336
 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S2 --R1 S2/R1.fq --R2 S2/R2.fq
-[18:37:32] This is snippy 4.6.0
-[18:37:32] Written by Torsten Seemann
-[18:37:32] Obtained from https://github.com/tseemann/snippy
-[18:37:32] Detected operating system: linux
-[18:37:32] Enabling bundled linux tools.
-[18:37:32] Found bwa - /usr/bin/bwa
-[18:37:32] Found bcftools - /usr/bin/bcftools
-[18:37:32] Found samtools - /usr/bin/samtools
-[18:37:32] Found java - /usr/bin/java
-[18:37:32] Found snpEff - /usr/bin/snpEff
-[18:37:32] Found samclip - /usr/bin/samclip
-[18:37:32] Found seqtk - /usr/bin/seqtk
-[18:37:32] Found parallel - /usr/bin/parallel
-[18:37:32] Found freebayes - /usr/bin/freebayes
-[18:37:33] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
-[18:37:33] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
-[18:37:33] Found vcfstreamsort - /usr/bin/vcfstreamsort
-[18:37:33] Found vcfuniq - /usr/bin/vcfuniq
-[18:37:33] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
-[18:37:33] Found gzip - /usr/bin/gzip
-[18:37:33] Found vt - /usr/bin/vt
-[18:37:33] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
-[18:37:33] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
-[18:37:33] Checking version: samtools --version is >= 1.7 - ok, have 1.21
-[18:37:33] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
-[18:37:33] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
-[18:37:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
-[18:37:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
-[18:37:34] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
-[18:37:34] Treating reference as 'fasta' format.
-[18:37:34] Will use 2 CPU cores.
-[18:37:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq
-[18:37:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq
-[18:37:34] Used --force, will overwrite existing S2
-[18:37:34] Changing working directory: S2
-[18:37:34] Creating reference folder: reference
-[18:37:34] Extracting FASTA and GFF from reference.
-[18:37:34] Wrote 3 sequences to ref.fa
-[18:37:34] Wrote 0 features to ref.gff
-[18:37:34] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
-[18:37:34] Using BAM RG (Read Group) ID: S2
-[18:37:34] Running: samtools faidx reference/ref.fa 2>> snps.log
-[18:37:34] Running: bwa index reference/ref.fa 2>> snps.log
-[18:37:34] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
-[18:37:34] Running: ln -sf reference/ref.fa . 2>> snps.log
-[18:37:34] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
-[18:37:34] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
-[18:37:34] Running: bwa mem  -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
+[14:16:29] This is snippy 4.6.0
+[14:16:29] Written by Torsten Seemann
+[14:16:29] Obtained from https://github.com/tseemann/snippy
+[14:16:29] Detected operating system: linux
+[14:16:29] Enabling bundled linux tools.
+[14:16:29] Found bwa - /usr/bin/bwa
+[14:16:29] Found bcftools - /usr/bin/bcftools
+[14:16:29] Found samtools - /usr/bin/samtools
+[14:16:29] Found java - /usr/bin/java
+[14:16:29] Found snpEff - /usr/bin/snpEff
+[14:16:29] Found samclip - /usr/bin/samclip
+[14:16:29] Found seqtk - /usr/bin/seqtk
+[14:16:29] Found parallel - /usr/bin/parallel
+[14:16:29] Found freebayes - /usr/bin/freebayes
+[14:16:29] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
+[14:16:29] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
+[14:16:29] Found vcfstreamsort - /usr/bin/vcfstreamsort
+[14:16:29] Found vcfuniq - /usr/bin/vcfuniq
+[14:16:29] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
+[14:16:29] Found gzip - /usr/bin/gzip
+[14:16:29] Found vt - /usr/bin/vt
+[14:16:29] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
+[14:16:29] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
+[14:16:29] Checking version: samtools --version is >= 1.7 - ok, have 1.21
+[14:16:29] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
+[14:16:29] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
+[14:16:30] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
+[14:16:30] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
+[14:16:30] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
+[14:16:30] Treating reference as 'fasta' format.
+[14:16:30] Will use 2 CPU cores.
+[14:16:30] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq
+[14:16:30] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq
+[14:16:30] Used --force, will overwrite existing S2
+[14:16:30] Changing working directory: S2
+[14:16:30] Creating reference folder: reference
+[14:16:30] Extracting FASTA and GFF from reference.
+[14:16:30] Wrote 3 sequences to ref.fa
+[14:16:30] Wrote 0 features to ref.gff
+[14:16:30] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
+[14:16:30] Using BAM RG (Read Group) ID: S2
+[14:16:30] Running: samtools faidx reference/ref.fa 2>> snps.log
+[14:16:30] Running: bwa index reference/ref.fa 2>> snps.log
+[14:16:30] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
+[14:16:30] Running: ln -sf reference/ref.fa . 2>> snps.log
+[14:16:30] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
+[14:16:30] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
+[14:16:30] Running: bwa mem  -Y -M -R '@RG\tID:S2\tSM:S2' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
 [M::bwa_idx_load_from_disk] read 0 ALT contigs
+[M::process] read 24000 sequences (2400000 bp)...
 [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
 [samclip] Loading: reference/ref.fa.fai
 [samclip] Found 3 sequences in reference/ref.fa.fai
-[M::process] read 24000 sequences (2400000 bp)...
 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11598, 0, 0)
 [M::mem_pestat] skip orientation FF as there are not enough pairs
 [M::mem_pestat] analyzing insert size distribution for orientation FR...
@@ -2692,17 +2728,17 @@
 [M::mem_pestat] low and high boundaries for proper pairs: (1, 433)
 [M::mem_pestat] skip orientation RF as there are not enough pairs
 [M::mem_pestat] skip orientation RR as there are not enough pairs
-[M::mem_process_seqs] Processed 24000 reads in 1.255 CPU sec, 1.901 real sec
+[M::mem_process_seqs] Processed 24000 reads in 1.424 CPU sec, 0.714 real sec
 [main] Version: 0.7.18-r1243-dirty
 [main] CMD: bwa mem -Y -M -R @RG\tID:S2\tSM:S2 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S2/R2.fq
-[main] Real time: 2.102 sec; CPU: 1.282 sec
+[main] Real time: 0.863 sec; CPU: 1.487 sec
 [samclip] Total SAM records 24000, removed 13, allowed 371, passed 23987
 [samclip] Header contained 6 lines
 [samclip] Done.
-[18:37:37] Running: samtools index snps.bam 2>> snps.log
-[18:37:37] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
-[18:37:37] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
-[18:37:41] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
+[14:16:31] Running: samtools index snps.bam 2>> snps.log
+[14:16:31] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
+[14:16:31] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
+[14:16:33] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
 normalize v0.5
 
 options:     input VCF file                                  -
@@ -2737,45 +2773,45 @@
        total no. variants observed              : 246
        total no. reference observed             : 0
 
-Time elapsed: 0.00s
+Time elapsed: 0.01s
 
-[18:37:41] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
-[18:37:41] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
-[18:37:41] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
-[18:37:41] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
-[18:37:41] Running: bcftools index -f snps.vcf.gz 2>> snps.log
-[18:37:41] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
-[18:37:41] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
-[18:37:41] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
-[18:37:41] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
-[18:37:41] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
-[18:37:41] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
-[18:37:42] Marked 841 heterozygous sites with 'n'
-[18:37:42] Creating extra output files: BED GFF CSV TXT HTML
-[18:37:42] Identified 246 variants.
-[18:37:42] Result folder: S2
-[18:37:42] Result files:
-[18:37:42] * S2/snps.aligned.fa
-[18:37:42] * S2/snps.bam
-[18:37:42] * S2/snps.bam.bai
-[18:37:42] * S2/snps.bed
-[18:37:42] * S2/snps.consensus.fa
-[18:37:42] * S2/snps.consensus.subs.fa
-[18:37:42] * S2/snps.csv
-[18:37:42] * S2/snps.filt.vcf
-[18:37:42] * S2/snps.gff
-[18:37:42] * S2/snps.html
-[18:37:42] * S2/snps.log
-[18:37:42] * S2/snps.raw.vcf
-[18:37:42] * S2/snps.subs.vcf
-[18:37:42] * S2/snps.tab
-[18:37:42] * S2/snps.txt
-[18:37:42] * S2/snps.vcf
-[18:37:42] * S2/snps.vcf.gz
-[18:37:42] * S2/snps.vcf.gz.csi
-[18:37:42] Walltime used: 10 seconds
-[18:37:42] May the SNPs be with you.
-[18:37:42] Done.
+[14:16:33] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
+[14:16:33] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
+[14:16:33] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
+[14:16:33] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
+[14:16:33] Running: bcftools index -f snps.vcf.gz 2>> snps.log
+[14:16:33] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
+[14:16:33] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
+[14:16:33] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
+[14:16:33] Running: bcftools consensus --sample S2 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
+[14:16:33] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
+[14:16:33] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
+[14:16:33] Marked 841 heterozygous sites with 'n'
+[14:16:33] Creating extra output files: BED GFF CSV TXT HTML
+[14:16:33] Identified 246 variants.
+[14:16:33] Result folder: S2
+[14:16:33] Result files:
+[14:16:33] * S2/snps.aligned.fa
+[14:16:33] * S2/snps.bam
+[14:16:33] * S2/snps.bam.bai
+[14:16:33] * S2/snps.bed
+[14:16:33] * S2/snps.consensus.fa
+[14:16:33] * S2/snps.consensus.subs.fa
+[14:16:33] * S2/snps.csv
+[14:16:33] * S2/snps.filt.vcf
+[14:16:33] * S2/snps.gff
+[14:16:33] * S2/snps.html
+[14:16:33] * S2/snps.log
+[14:16:33] * S2/snps.raw.vcf
+[14:16:33] * S2/snps.subs.vcf
+[14:16:33] * S2/snps.tab
+[14:16:33] * S2/snps.txt
+[14:16:33] * S2/snps.vcf
+[14:16:33] * S2/snps.vcf.gz
+[14:16:33] * S2/snps.vcf.gz.csi
+[14:16:33] Walltime used: 4 seconds
+[14:16:33] Questionable SNP? Try the --report option to see the alignments.
+[14:16:33] Done.
 mkdir -p S3
 wgsim -S 3 \
          -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
@@ -2784,59 +2820,59 @@
 [wgsim_core] calculating the total length of the reference sequence...
 [wgsim_core] 3 sequences, total length: 317336
 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S3 --R1 S3/R1.fq --R2 S3/R2.fq
-[18:37:43] This is snippy 4.6.0
-[18:37:43] Written by Torsten Seemann
-[18:37:43] Obtained from https://github.com/tseemann/snippy
-[18:37:43] Detected operating system: linux
-[18:37:43] Enabling bundled linux tools.
-[18:37:43] Found bwa - /usr/bin/bwa
-[18:37:43] Found bcftools - /usr/bin/bcftools
-[18:37:43] Found samtools - /usr/bin/samtools
-[18:37:43] Found java - /usr/bin/java
-[18:37:43] Found snpEff - /usr/bin/snpEff
-[18:37:43] Found samclip - /usr/bin/samclip
-[18:37:43] Found seqtk - /usr/bin/seqtk
-[18:37:43] Found parallel - /usr/bin/parallel
-[18:37:43] Found freebayes - /usr/bin/freebayes
-[18:37:43] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
-[18:37:43] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
-[18:37:43] Found vcfstreamsort - /usr/bin/vcfstreamsort
-[18:37:43] Found vcfuniq - /usr/bin/vcfuniq
-[18:37:43] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
-[18:37:43] Found gzip - /usr/bin/gzip
-[18:37:43] Found vt - /usr/bin/vt
-[18:37:43] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
-[18:37:44] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
-[18:37:44] Checking version: samtools --version is >= 1.7 - ok, have 1.21
-[18:37:44] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
-[18:37:44] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
-[18:37:44] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
-[18:37:44] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
-[18:37:44] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
-[18:37:44] Treating reference as 'fasta' format.
-[18:37:44] Will use 2 CPU cores.
-[18:37:44] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq
-[18:37:44] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq
-[18:37:44] Used --force, will overwrite existing S3
-[18:37:44] Changing working directory: S3
-[18:37:44] Creating reference folder: reference
-[18:37:44] Extracting FASTA and GFF from reference.
-[18:37:44] Wrote 3 sequences to ref.fa
-[18:37:44] Wrote 0 features to ref.gff
-[18:37:44] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
-[18:37:44] Using BAM RG (Read Group) ID: S3
-[18:37:44] Running: samtools faidx reference/ref.fa 2>> snps.log
-[18:37:44] Running: bwa index reference/ref.fa 2>> snps.log
-[18:37:45] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
-[18:37:45] Running: ln -sf reference/ref.fa . 2>> snps.log
-[18:37:45] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
-[18:37:45] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
-[18:37:45] Running: bwa mem  -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
+[14:16:34] This is snippy 4.6.0
+[14:16:34] Written by Torsten Seemann
+[14:16:34] Obtained from https://github.com/tseemann/snippy
+[14:16:34] Detected operating system: linux
+[14:16:34] Enabling bundled linux tools.
+[14:16:34] Found bwa - /usr/bin/bwa
+[14:16:34] Found bcftools - /usr/bin/bcftools
+[14:16:34] Found samtools - /usr/bin/samtools
+[14:16:34] Found java - /usr/bin/java
+[14:16:34] Found snpEff - /usr/bin/snpEff
+[14:16:34] Found samclip - /usr/bin/samclip
+[14:16:34] Found seqtk - /usr/bin/seqtk
+[14:16:34] Found parallel - /usr/bin/parallel
+[14:16:34] Found freebayes - /usr/bin/freebayes
+[14:16:34] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
+[14:16:34] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
+[14:16:34] Found vcfstreamsort - /usr/bin/vcfstreamsort
+[14:16:34] Found vcfuniq - /usr/bin/vcfuniq
+[14:16:34] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
+[14:16:34] Found gzip - /usr/bin/gzip
+[14:16:34] Found vt - /usr/bin/vt
+[14:16:34] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
+[14:16:34] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
+[14:16:34] Checking version: samtools --version is >= 1.7 - ok, have 1.21
+[14:16:34] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
+[14:16:34] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
+[14:16:34] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
+[14:16:34] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
+[14:16:34] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
+[14:16:34] Treating reference as 'fasta' format.
+[14:16:34] Will use 2 CPU cores.
+[14:16:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq
+[14:16:34] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq
+[14:16:34] Used --force, will overwrite existing S3
+[14:16:34] Changing working directory: S3
+[14:16:34] Creating reference folder: reference
+[14:16:34] Extracting FASTA and GFF from reference.
+[14:16:34] Wrote 3 sequences to ref.fa
+[14:16:34] Wrote 0 features to ref.gff
+[14:16:34] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
+[14:16:34] Using BAM RG (Read Group) ID: S3
+[14:16:34] Running: samtools faidx reference/ref.fa 2>> snps.log
+[14:16:34] Running: bwa index reference/ref.fa 2>> snps.log
+[14:16:34] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
+[14:16:34] Running: ln -sf reference/ref.fa . 2>> snps.log
+[14:16:34] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
+[14:16:34] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
+[14:16:34] Running: bwa mem  -Y -M -R '@RG\tID:S3\tSM:S3' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
 [M::bwa_idx_load_from_disk] read 0 ALT contigs
+[M::process] read 24000 sequences (2400000 bp)...
 [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
 [samclip] Loading: reference/ref.fa.fai
 [samclip] Found 3 sequences in reference/ref.fa.fai
-[M::process] read 24000 sequences (2400000 bp)...
 [M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 11590, 0, 0)
 [M::mem_pestat] skip orientation FF as there are not enough pairs
 [M::mem_pestat] analyzing insert size distribution for orientation FR...
@@ -2846,17 +2882,17 @@
 [M::mem_pestat] low and high boundaries for proper pairs: (1, 436)
 [M::mem_pestat] skip orientation RF as there are not enough pairs
 [M::mem_pestat] skip orientation RR as there are not enough pairs
-[M::mem_process_seqs] Processed 24000 reads in 1.262 CPU sec, 2.236 real sec
+[M::mem_process_seqs] Processed 24000 reads in 1.375 CPU sec, 0.689 real sec
 [main] Version: 0.7.18-r1243-dirty
 [main] CMD: bwa mem -Y -M -R @RG\tID:S3\tSM:S3 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S3/R2.fq
-[main] Real time: 2.496 sec; CPU: 1.287 sec
+[main] Real time: 0.869 sec; CPU: 1.445 sec
 [samclip] Total SAM records 24000, removed 30, allowed 356, passed 23970
 [samclip] Header contained 6 lines
 [samclip] Done.
-[18:37:48] Running: samtools index snps.bam 2>> snps.log
-[18:37:48] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
-[18:37:48] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
-[18:37:51] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
+[14:16:36] Running: samtools index snps.bam 2>> snps.log
+[14:16:36] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
+[14:16:36] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
+[14:16:37] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
 normalize v0.5
 
 options:     input VCF file                                  -
@@ -2891,45 +2927,45 @@
        total no. variants observed              : 254
        total no. reference observed             : 0
 
-Time elapsed: 0.00s
+Time elapsed: 0.01s
 
-[18:37:51] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
-[18:37:52] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
-[18:37:52] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
-[18:37:52] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
-[18:37:52] Running: bcftools index -f snps.vcf.gz 2>> snps.log
-[18:37:52] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
-[18:37:52] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
-[18:37:52] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
-[18:37:52] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
-[18:37:52] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
-[18:37:52] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
-[18:37:53] Marked 846 heterozygous sites with 'n'
-[18:37:53] Creating extra output files: BED GFF CSV TXT HTML
-[18:37:53] Identified 254 variants.
-[18:37:53] Result folder: S3
-[18:37:53] Result files:
-[18:37:53] * S3/snps.aligned.fa
-[18:37:53] * S3/snps.bam
-[18:37:53] * S3/snps.bam.bai
-[18:37:53] * S3/snps.bed
-[18:37:53] * S3/snps.consensus.fa
-[18:37:53] * S3/snps.consensus.subs.fa
-[18:37:53] * S3/snps.csv
-[18:37:53] * S3/snps.filt.vcf
-[18:37:53] * S3/snps.gff
-[18:37:53] * S3/snps.html
-[18:37:53] * S3/snps.log
-[18:37:53] * S3/snps.raw.vcf
-[18:37:53] * S3/snps.subs.vcf
-[18:37:53] * S3/snps.tab
-[18:37:53] * S3/snps.txt
-[18:37:53] * S3/snps.vcf
-[18:37:53] * S3/snps.vcf.gz
-[18:37:53] * S3/snps.vcf.gz.csi
-[18:37:53] Walltime used: 10 seconds
-[18:37:53] Did you know? Snippy is a combination of SNP, Skippy, and snappy.
-[18:37:53] Done.
+[14:16:37] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
+[14:16:37] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
+[14:16:37] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
+[14:16:37] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
+[14:16:37] Running: bcftools index -f snps.vcf.gz 2>> snps.log
+[14:16:37] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
+[14:16:37] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
+[14:16:38] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
+[14:16:38] Running: bcftools consensus --sample S3 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
+[14:16:38] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
+[14:16:38] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
+[14:16:38] Marked 846 heterozygous sites with 'n'
+[14:16:38] Creating extra output files: BED GFF CSV TXT HTML
+[14:16:38] Identified 254 variants.
+[14:16:38] Result folder: S3
+[14:16:38] Result files:
+[14:16:38] * S3/snps.aligned.fa
+[14:16:38] * S3/snps.bam
+[14:16:38] * S3/snps.bam.bai
+[14:16:38] * S3/snps.bed
+[14:16:38] * S3/snps.consensus.fa
+[14:16:38] * S3/snps.consensus.subs.fa
+[14:16:38] * S3/snps.csv
+[14:16:38] * S3/snps.filt.vcf
+[14:16:38] * S3/snps.gff
+[14:16:38] * S3/snps.html
+[14:16:38] * S3/snps.log
+[14:16:38] * S3/snps.raw.vcf
+[14:16:38] * S3/snps.subs.vcf
+[14:16:38] * S3/snps.tab
+[14:16:38] * S3/snps.txt
+[14:16:38] * S3/snps.vcf
+[14:16:38] * S3/snps.vcf.gz
+[14:16:38] * S3/snps.vcf.gz.csi
+[14:16:38] Walltime used: 4 seconds
+[14:16:38] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues
+[14:16:38] Done.
 mkdir -p S4
 wgsim -S 4 \
          -h -r 0.005 -N 12000 -1 100 -2 100 -d 200 \
@@ -2938,54 +2974,54 @@
 [wgsim_core] calculating the total length of the reference sequence...
 [wgsim_core] 3 sequences, total length: 317336
 ../bin/snippy --cpus 2 --ram 2 --force --ref example.fna --outdir S4 --R1 S4/R1.fq --R2 S4/R2.fq
-[18:37:53] This is snippy 4.6.0
-[18:37:53] Written by Torsten Seemann
-[18:37:53] Obtained from https://github.com/tseemann/snippy
-[18:37:53] Detected operating system: linux
-[18:37:53] Enabling bundled linux tools.
-[18:37:53] Found bwa - /usr/bin/bwa
-[18:37:53] Found bcftools - /usr/bin/bcftools
-[18:37:53] Found samtools - /usr/bin/samtools
-[18:37:53] Found java - /usr/bin/java
-[18:37:53] Found snpEff - /usr/bin/snpEff
-[18:37:53] Found samclip - /usr/bin/samclip
-[18:37:53] Found seqtk - /usr/bin/seqtk
-[18:37:53] Found parallel - /usr/bin/parallel
-[18:37:53] Found freebayes - /usr/bin/freebayes
-[18:37:53] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
-[18:37:53] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
-[18:37:53] Found vcfstreamsort - /usr/bin/vcfstreamsort
-[18:37:53] Found vcfuniq - /usr/bin/vcfuniq
-[18:37:53] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
-[18:37:53] Found gzip - /usr/bin/gzip
-[18:37:53] Found vt - /usr/bin/vt
-[18:37:53] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
-[18:37:54] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
-[18:37:54] Checking version: samtools --version is >= 1.7 - ok, have 1.21
-[18:37:54] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
-[18:37:54] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
-[18:37:54] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
-[18:37:54] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
-[18:37:54] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
-[18:37:54] Treating reference as 'fasta' format.
-[18:37:54] Will use 2 CPU cores.
-[18:37:54] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq
-[18:37:54] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq
-[18:37:54] Used --force, will overwrite existing S4
-[18:37:54] Changing working directory: S4
-[18:37:54] Creating reference folder: reference
-[18:37:54] Extracting FASTA and GFF from reference.
-[18:37:54] Wrote 3 sequences to ref.fa
-[18:37:54] Wrote 0 features to ref.gff
-[18:37:54] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
-[18:37:54] Using BAM RG (Read Group) ID: S4
-[18:37:54] Running: samtools faidx reference/ref.fa 2>> snps.log
-[18:37:54] Running: bwa index reference/ref.fa 2>> snps.log
-[18:37:54] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
-[18:37:54] Running: ln -sf reference/ref.fa . 2>> snps.log
-[18:37:55] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
-[18:37:55] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
-[18:37:55] Running: bwa mem  -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
+[14:16:38] This is snippy 4.6.0
+[14:16:38] Written by Torsten Seemann
+[14:16:38] Obtained from https://github.com/tseemann/snippy
+[14:16:38] Detected operating system: linux
+[14:16:38] Enabling bundled linux tools.
+[14:16:38] Found bwa - /usr/bin/bwa
+[14:16:38] Found bcftools - /usr/bin/bcftools
+[14:16:38] Found samtools - /usr/bin/samtools
+[14:16:38] Found java - /usr/bin/java
+[14:16:38] Found snpEff - /usr/bin/snpEff
+[14:16:38] Found samclip - /usr/bin/samclip
+[14:16:38] Found seqtk - /usr/bin/seqtk
+[14:16:38] Found parallel - /usr/bin/parallel
+[14:16:38] Found freebayes - /usr/bin/freebayes
+[14:16:38] Found freebayes-parallel - /usr/share/freebayes/scripts/freebayes-parallel
+[14:16:38] Found fasta_generate_regions.py - /usr/share/freebayes/scripts/fasta_generate_regions.py
+[14:16:38] Found vcfstreamsort - /usr/bin/vcfstreamsort
+[14:16:38] Found vcfuniq - /usr/bin/vcfuniq
+[14:16:38] Found vcffirstheader - /usr/share/freebayes/scripts/vcffirstheader
+[14:16:38] Found gzip - /usr/bin/gzip
+[14:16:38] Found vt - /usr/bin/vt
+[14:16:38] Found snippy-vcf_to_tab - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab
+[14:16:38] Found snippy-vcf_report - /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_report
+[14:16:38] Checking version: samtools --version is >= 1.7 - ok, have 1.21
+[14:16:38] Checking version: bcftools --version is >= 1.7 - ok, have 1.21
+[14:16:38] Checking version: freebayes --version is >= 1.1 - ok, have 1.3.8
+[14:16:38] Checking version: snpEff -version is >= 4.3 - ok, have 5.2
+[14:16:38] Checking version: bwa is >= 0.7.12 - ok, have 0.7.18
+[14:16:38] Using reference: /build/reproducible-path/snippy-4.6.0+dfsg/test/example.fna
+[14:16:38] Treating reference as 'fasta' format.
+[14:16:38] Will use 2 CPU cores.
+[14:16:38] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq
+[14:16:38] Using read file: /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq
+[14:16:38] Used --force, will overwrite existing S4
+[14:16:38] Changing working directory: S4
+[14:16:38] Creating reference folder: reference
+[14:16:38] Extracting FASTA and GFF from reference.
+[14:16:39] Wrote 3 sequences to ref.fa
+[14:16:39] Wrote 0 features to ref.gff
+[14:16:39] Freebayes will process 3 chunks of 107589 bp, 2 chunks at a time.
+[14:16:39] Using BAM RG (Read Group) ID: S4
+[14:16:39] Running: samtools faidx reference/ref.fa 2>> snps.log
+[14:16:39] Running: bwa index reference/ref.fa 2>> snps.log
+[14:16:39] Running: mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa 2>> snps.log
+[14:16:39] Running: ln -sf reference/ref.fa . 2>> snps.log
+[14:16:39] Running: ln -sf reference/ref.fa.fai . 2>> snps.log
+[14:16:39] Running: mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz 2>> snps.log
+[14:16:39] Running: bwa mem  -Y -M -R '@RG\tID:S4\tSM:S4' -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp --threads 0 -m 2000M | samtools fixmate -m --threads 0 - - | samtools sort -l 0 -T /tmp --threads 0 -m 2000M | samtools markdup -T /tmp --threads 0 -r -s - - > snps.bam 2>> snps.log
 [M::bwa_idx_load_from_disk] read 0 ALT contigs
 [M::process] read 24000 sequences (2400000 bp)...
 [samclip] samclip 0.4.0 by Torsten Seemann (@torstenseemann)
@@ -3000,17 +3036,17 @@
 [M::mem_pestat] low and high boundaries for proper pairs: (1, 425)
 [M::mem_pestat] skip orientation RF as there are not enough pairs
 [M::mem_pestat] skip orientation RR as there are not enough pairs
-[M::mem_process_seqs] Processed 24000 reads in 1.226 CPU sec, 1.230 real sec
+[M::mem_process_seqs] Processed 24000 reads in 1.466 CPU sec, 0.737 real sec
 [main] Version: 0.7.18-r1243-dirty
 [main] CMD: bwa mem -Y -M -R @RG\tID:S4\tSM:S4 -t 2 reference/ref.fa /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R1.fq /build/reproducible-path/snippy-4.6.0+dfsg/test/S4/R2.fq
-[main] Real time: 1.563 sec; CPU: 1.252 sec
+[main] Real time: 0.834 sec; CPU: 1.530 sec
 [samclip] Total SAM records 24000, removed 26, allowed 396, passed 23974
 [samclip] Header contained 6 lines
 [samclip] Done.
-[18:37:57] Running: samtools index snps.bam 2>> snps.log
-[18:37:57] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
-[18:37:57] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
-[18:38:00] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
+[14:16:40] Running: samtools index snps.bam 2>> snps.log
+[14:16:40] Running: fasta_generate_regions.py reference/ref.fa.fai 107589 > reference/ref.txt 2>> snps.log
+[14:16:40] Running: freebayes-parallel reference/ref.txt 2 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
+[14:16:42] Running: bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf  | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf 2>> snps.log
 normalize v0.5
 
 options:     input VCF file                                  -
@@ -3045,45 +3081,45 @@
        total no. variants observed              : 257
        total no. reference observed             : 0
 
-Time elapsed: 0.00s
+Time elapsed: 0.01s
 
-[18:38:00] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
-[18:38:00] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
-[18:38:00] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
-[18:38:00] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
-[18:38:00] Running: bcftools index -f snps.vcf.gz 2>> snps.log
-[18:38:00] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
-[18:38:00] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
-[18:38:00] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
-[18:38:00] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
-[18:38:00] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
-[18:38:00] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
-[18:38:01] Marked 799 heterozygous sites with 'n'
-[18:38:01] Creating extra output files: BED GFF CSV TXT HTML
-[18:38:01] Identified 257 variants.
-[18:38:01] Result folder: S4
-[18:38:01] Result files:
-[18:38:01] * S4/snps.aligned.fa
-[18:38:01] * S4/snps.bam
-[18:38:01] * S4/snps.bam.bai
-[18:38:01] * S4/snps.bed
-[18:38:01] * S4/snps.consensus.fa
-[18:38:01] * S4/snps.consensus.subs.fa
-[18:38:01] * S4/snps.csv
-[18:38:01] * S4/snps.filt.vcf
-[18:38:01] * S4/snps.gff
-[18:38:01] * S4/snps.html
-[18:38:01] * S4/snps.log
-[18:38:01] * S4/snps.raw.vcf
-[18:38:01] * S4/snps.subs.vcf
-[18:38:01] * S4/snps.tab
-[18:38:01] * S4/snps.txt
-[18:38:01] * S4/snps.vcf
-[18:38:01] * S4/snps.vcf.gz
-[18:38:01] * S4/snps.vcf.gz.csi
-[18:38:01] Walltime used: 8 seconds
-[18:38:01] Have a suggestion? Tell me at https://github.com/tseemann/snippy/issues
-[18:38:01] Done.
+[14:16:42] Running: cp snps.filt.vcf snps.vcf 2>> snps.log
+[14:16:42] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab 2>> snps.log
+[14:16:42] Running: /build/reproducible-path/snippy-4.6.0+dfsg/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf 2>> snps.log
+[14:16:42] Running: bcftools convert -Oz -o snps.vcf.gz snps.vcf 2>> snps.log
+[14:16:42] Running: bcftools index -f snps.vcf.gz 2>> snps.log
+[14:16:42] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz 2>> snps.log
+[14:16:42] Running: bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf 2>> snps.log
+[14:16:42] Running: bcftools index -f snps.subs.vcf.gz 2>> snps.log
+[14:16:42] Running: bcftools consensus --sample S4 -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz 2>> snps.log
+[14:16:42] Running: rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi 2>> snps.log
+[14:16:42] Generating reference aligned/masked FASTA relative to reference: snps.aligned.fa
+[14:16:42] Marked 799 heterozygous sites with 'n'
+[14:16:42] Creating extra output files: BED GFF CSV TXT HTML
+[14:16:42] Identified 257 variants.
+[14:16:42] Result folder: S4
+[14:16:42] Result files:
+[14:16:42] * S4/snps.aligned.fa
+[14:16:42] * S4/snps.bam
+[14:16:42] * S4/snps.bam.bai
+[14:16:42] * S4/snps.bed
+[14:16:42] * S4/snps.consensus.fa
+[14:16:42] * S4/snps.consensus.subs.fa
+[14:16:42] * S4/snps.csv
+[14:16:42] * S4/snps.filt.vcf
+[14:16:42] * S4/snps.gff
+[14:16:42] * S4/snps.html
+[14:16:42] * S4/snps.log
+[14:16:42] * S4/snps.raw.vcf
+[14:16:42] * S4/snps.subs.vcf
+[14:16:42] * S4/snps.tab
+[14:16:42] * S4/snps.txt
+[14:16:42] * S4/snps.vcf
+[14:16:42] * S4/snps.vcf.gz
+[14:16:42] * S4/snps.vcf.gz.csi
+[14:16:42] Walltime used: 4 seconds
+[14:16:42] Did you know? Snippy is a combination of SNP, Skippy, and snappy.
+[14:16:42] Done.
 ../bin/snippy-core --prefix core --ref example.fna S1 S2 S3 S4
 ../bin/snippy-core --prefix core-mask --ref example.fna --mask example.bed S1 S2 S3 S4
 This is snippy-core 4.6.0
@@ -3116,7 +3152,7 @@
 Generating core.full.aln
 Creating TSV file: core.txt
 Running: snp-sites -c -o core.aln core.full.aln
-You can mask columns using '--mask BEDFILE --mask-char X'
+The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md
 Done.
 This is snippy-core 4.6.0
 Obtained from http://github.com/tseemann/snippy
@@ -3150,7 +3186,7 @@
 Generating core-mask.full.aln
 Creating TSV file: core-mask.txt
 Running: snp-sites -c -o core-mask.aln core-mask.full.aln
-You can mask columns using '--mask BEDFILE --mask-char X'
+The Snippy manual is at http://github.com/tseemann/snippy/blob/master/README.md
 Done.
 wc -l S?/snps.tab
   262 S1/snps.tab
@@ -3188,12 +3224,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/671649/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/671649/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/1272158 and its subdirectories
-I: Current time: Thu Mar 26 18:38:11 -12 2026
-I: pbuilder-time-stamp: 1774593491
+I: removing directory /srv/workspace/pbuilder/671649 and its subdirectories
+I: Current time: Sat Feb 22 14:16:48 +14 2025
+I: pbuilder-time-stamp: 1740183408