I: pbuilder: network access will be disabled during build
I: Current time: Wed Feb 26 09:03:16 +14 2025
I: pbuilder-time-stamp: 1740510196
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc]
I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz]
I: copying [./tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc: unsupported subcommand
dpkg-source: info: extracting tvc in tvc-5.0.3+git20151221.80e144e+dfsg
dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz
dpkg-source: info: unpacking tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying cmake.patch
dpkg-source: info: applying bamtools.patch
dpkg-source: info: applying help.patch
dpkg-source: info: applying hurd.patch
dpkg-source: info: applying sse.patch
dpkg-source: info: applying use_debian_packaged_smithwaterman.patch
dpkg-source: info: applying python3.patch
dpkg-source: info: applying gcc11.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/4010158/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 25 19:03 /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/4010158/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/4010158/tmp/hooks/D02_print_environment starting
I: set
  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 '
  DIRSTACK=()
  DISTRIBUTION=unstable
  EUID=0
  FUNCNAME=([0]="Echo" [1]="main")
  GROUPS=()
  HOME=/root
  HOSTNAME=i-capture-the-hostname
  HOSTTYPE=aarch64
  HOST_ARCH=arm64
  IFS=' 	
  '
  INVOCATION_ID=71d254529c2849e8867aabc83383191d
  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=4010158
  PS4='+ '
  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.hl9scNme/pbuilderrc_GPlr --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.hl9scNme/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+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 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 14:40 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/4010158/tmp/hooks/D02_print_environment finished
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: arm64
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19889 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
 pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
  Package debhelper-compat is not installed.
 pbuilder-satisfydepends-dummy depends on cmake; however:
  Package cmake is not installed.
 pbuilder-satisfydepends-dummy depends on libbamtools-dev; however:
  Package libbamtools-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however:
  Package libjsoncpp-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libarmadillo-dev; however:
  Package libarmadillo-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libboost-math-dev; however:
  Package libboost-math-dev is not installed.
 pbuilder-satisfydepends-dummy depends on libsmithwaterman-dev; however:
  Package libsmithwaterman-dev is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
  autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libarmadillo-dev{a} libarmadillo14{a} libarpack2-dev{a} libarpack2t64{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas-dev{a} libblas3{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdisorder-dev{a} libdisorder0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgnutls30t64{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-310{a} libhdf5-cpp-310{a} libhdf5-dev{a} libhdf5-fortran-310{a} libhdf5-hl-310{a} libhdf5-hl-cpp-310{a} libhdf5-hl-fortran-310{a} libicu72{a} libidn2-0{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-dev{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libnghttp3-9{a} libnghttp3-dev{a} libp11-kit-dev{a} libp11-kit0{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsuperlu-dev{a} libsuperlu7{a} libsz2{a} libtasn1-6{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libunistring5{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} 
The following packages are RECOMMENDED but will NOT be installed:
  ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 
0 packages upgraded, 128 newly installed, 0 to remove and 0 not upgraded.
Need to get 74.8 MB of archives. After unpacking 430 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB]
Get: 2 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB]
Get: 3 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 5 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 6 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 7 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 8 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 9 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB]
Get: 11 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 12 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 13 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 14 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB]
Get: 15 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB]
Get: 17 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.6-1 [2268 kB]
Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB]
Get: 20 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.2+b1 [630 kB]
Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB]
Get: 22 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b6 [297 kB]
Get: 23 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-4 [32.2 kB]
Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B]
Get: 27 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-4 [308 kB]
Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 30 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB]
Get: 31 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB]
Get: 32 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB]
Get: 33 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB]
Get: 34 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB]
Get: 35 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.6.0-2 [60.5 kB]
Get: 36 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB]
Get: 37 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB]
Get: 38 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB]
Get: 39 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB]
Get: 40 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB]
Get: 41 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB]
Get: 42 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB]
Get: 43 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.12.1-2 [340 kB]
Get: 44 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 45 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB]
Get: 46 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB]
Get: 47 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB]
Get: 48 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.6-1 [9912 kB]
Get: 49 http://deb.debian.org/debian unstable/main arm64 comerr-dev arm64 2.1-1.47.2-1 [55.9 kB]
Get: 50 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 51 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-3 [539 kB]
Get: 52 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 53 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 54 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB]
Get: 55 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B]
Get: 56 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 57 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 58 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 59 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 60 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 61 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB]
Get: 62 http://deb.debian.org/debian unstable/main arm64 hdf5-helpers arm64 1.14.5+repack-3 [26.6 kB]
Get: 63 http://deb.debian.org/debian unstable/main arm64 libgssrpc4t64 arm64 1.21.3-4 [56.9 kB]
Get: 64 http://deb.debian.org/debian unstable/main arm64 libkadm5clnt-mit12 arm64 1.21.3-4 [41.0 kB]
Get: 65 http://deb.debian.org/debian unstable/main arm64 libkdb5-10t64 arm64 1.21.3-4 [41.0 kB]
Get: 66 http://deb.debian.org/debian unstable/main arm64 libkadm5srv-mit12 arm64 1.21.3-4 [53.1 kB]
Get: 67 http://deb.debian.org/debian unstable/main arm64 krb5-multidev arm64 1.21.3-4 [126 kB]
Get: 68 http://deb.debian.org/debian unstable/main arm64 libaec0 arm64 1.1.3-1+b1 [22.5 kB]
Get: 69 http://deb.debian.org/debian unstable/main arm64 libsz2 arm64 1.1.3-1+b1 [8044 B]
Get: 70 http://deb.debian.org/debian unstable/main arm64 libaec-dev arm64 1.1.3-1+b1 [20.2 kB]
Get: 71 http://deb.debian.org/debian unstable/main arm64 libblas3 arm64 3.12.1-2 [104 kB]
Get: 72 http://deb.debian.org/debian unstable/main arm64 libgfortran5 arm64 14.2.0-17 [361 kB]
Get: 73 http://deb.debian.org/debian unstable/main arm64 liblapack3 arm64 3.12.1-2 [1819 kB]
Get: 74 http://deb.debian.org/debian unstable/main arm64 libarpack2t64 arm64 3.9.1-4 [83.7 kB]
Get: 75 http://deb.debian.org/debian unstable/main arm64 libarmadillo14 arm64 1:14.2.3+dfsg-1 [102 kB]
Get: 76 http://deb.debian.org/debian unstable/main arm64 libblas-dev arm64 3.12.1-2 [111 kB]
Get: 77 http://deb.debian.org/debian unstable/main arm64 liblapack-dev arm64 3.12.1-2 [3726 kB]
Get: 78 http://deb.debian.org/debian unstable/main arm64 libarpack2-dev arm64 3.9.1-4 [102 kB]
Get: 79 http://deb.debian.org/debian unstable/main arm64 libhdf5-310 arm64 1.14.5+repack-3 [1155 kB]
Get: 80 http://deb.debian.org/debian unstable/main arm64 libhdf5-fortran-310 arm64 1.14.5+repack-3 [110 kB]
Get: 81 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-310 arm64 1.14.5+repack-3 [66.1 kB]
Get: 82 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-fortran-310 arm64 1.14.5+repack-3 [42.1 kB]
Get: 83 http://deb.debian.org/debian unstable/main arm64 libhdf5-cpp-310 arm64 1.14.5+repack-3 [121 kB]
Get: 84 http://deb.debian.org/debian unstable/main arm64 libhdf5-hl-cpp-310 arm64 1.14.5+repack-3 [24.4 kB]
Get: 85 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get: 86 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo arm64 1:2.1.5-3.1 [173 kB]
Get: 87 http://deb.debian.org/debian unstable/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-3.1 [293 kB]
Get: 88 http://deb.debian.org/debian unstable/main arm64 libjpeg-dev arm64 1:2.1.5-3.1 [72.0 kB]
Get: 89 http://deb.debian.org/debian unstable/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB]
Get: 90 http://deb.debian.org/debian unstable/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB]
Get: 91 http://deb.debian.org/debian unstable/main arm64 libkrb5-dev arm64 1.21.3-4 [15.9 kB]
Get: 92 http://deb.debian.org/debian unstable/main arm64 libldap-dev arm64 2.6.9+dfsg-1 [305 kB]
Get: 93 http://deb.debian.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get: 94 http://deb.debian.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get: 95 http://deb.debian.org/debian unstable/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get: 96 http://deb.debian.org/debian unstable/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB]
Get: 97 http://deb.debian.org/debian unstable/main arm64 libnghttp3-dev arm64 1.6.0-2 [86.5 kB]
Get: 98 http://deb.debian.org/debian unstable/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB]
Get: 99 http://deb.debian.org/debian unstable/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-3 [329 kB]
Get: 100 http://deb.debian.org/debian unstable/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-3 [621 kB]
Get: 101 http://deb.debian.org/debian unstable/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB]
Get: 102 http://deb.debian.org/debian unstable/main arm64 libunbound8 arm64 1.22.0-1+b1 [553 kB]
Get: 103 http://deb.debian.org/debian unstable/main arm64 libgnutls-dane0t64 arm64 3.8.9-2 [452 kB]
Get: 104 http://deb.debian.org/debian unstable/main arm64 libgnutls-openssl27t64 arm64 3.8.9-2 [452 kB]
Get: 105 http://deb.debian.org/debian unstable/main arm64 libp11-kit-dev arm64 0.25.5-3 [208 kB]
Get: 106 http://deb.debian.org/debian unstable/main arm64 libtasn1-6-dev arm64 4.20.0-2 [96.7 kB]
Get: 107 http://deb.debian.org/debian unstable/main arm64 nettle-dev arm64 3.10.1-1 [1325 kB]
Get: 108 http://deb.debian.org/debian unstable/main arm64 libgnutls28-dev arm64 3.8.9-2 [1419 kB]
Get: 109 http://deb.debian.org/debian unstable/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB]
Get: 110 http://deb.debian.org/debian unstable/main arm64 libssl-dev arm64 3.4.1-1 [3232 kB]
Get: 111 http://deb.debian.org/debian unstable/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB]
Get: 112 http://deb.debian.org/debian unstable/main arm64 libzstd-dev arm64 1.5.6+dfsg-2 [329 kB]
Get: 113 http://deb.debian.org/debian unstable/main arm64 libcurl4-openssl-dev arm64 8.12.1-2 [468 kB]
Get: 114 http://deb.debian.org/debian unstable/main arm64 libhdf5-dev arm64 1.14.5+repack-3 [3225 kB]
Get: 115 http://deb.debian.org/debian unstable/main arm64 libsuperlu7 arm64 7.0.0+dfsg1-2 [144 kB]
Get: 116 http://deb.debian.org/debian unstable/main arm64 libsuperlu-dev arm64 7.0.0+dfsg1-2 [21.9 kB]
Get: 117 http://deb.debian.org/debian unstable/main arm64 libarmadillo-dev arm64 1:14.2.3+dfsg-1 [414 kB]
Get: 118 http://deb.debian.org/debian unstable/main arm64 libbamtools2.5.2 arm64 2.5.2+dfsg-6+b1 [141 kB]
Get: 119 http://deb.debian.org/debian unstable/main arm64 libbamtools-dev arm64 2.5.2+dfsg-6+b1 [210 kB]
Get: 120 http://deb.debian.org/debian unstable/main arm64 libboost1.83-dev arm64 1.83.0-4.1 [10.6 MB]
Get: 121 http://deb.debian.org/debian unstable/main arm64 libboost-math1.83.0 arm64 1.83.0-4.1 [471 kB]
Get: 122 http://deb.debian.org/debian unstable/main arm64 libboost-math1.83-dev arm64 1.83.0-4.1 [536 kB]
Get: 123 http://deb.debian.org/debian unstable/main arm64 libboost-math-dev arm64 1.83.0.2+b2 [3784 B]
Get: 124 http://deb.debian.org/debian unstable/main arm64 libdisorder0 arm64 0.0.2+git20130809.8062ee1-4+b2 [4920 B]
Get: 125 http://deb.debian.org/debian unstable/main arm64 libdisorder-dev arm64 0.0.2+git20130809.8062ee1-4+b2 [4888 B]
Get: 126 http://deb.debian.org/debian unstable/main arm64 libjsoncpp-dev arm64 1.9.6-3 [25.0 kB]
Get: 127 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman0 arm64 0.0+git20160702.2610e25-12+b2 [32.4 kB]
Get: 128 http://deb.debian.org/debian unstable/main arm64 libsmithwaterman-dev arm64 0.0+git20160702.2610e25-12+b2 [37.9 kB]
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I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+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  > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes
dpkg-buildpackage: info: source package tvc
dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Mohammed Bilal <mdbilal@disroot.org>
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CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required):
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-- The C compiler identification is GNU 14.2.0
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/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp
[ 37%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/MiscUtil.cpp
[ 39%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c
In file included from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64,
                 from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19:
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain<T>::optimal_path() [with T = long unsigned int]':
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:64:3:   required from 'void markov_chain<T>::initialize(_ForwardIterator, _ForwardIterator, T, T) [with _ForwardIterator = __gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >; T = long unsigned int]'
   64 |   optimal_path();
      |   ^~~~~~~~~~~~
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:38:13:   required from 'markov_chain<T>::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<long unsigned int*, std::vector<long unsigned int> >; T = long unsigned int]'
   38 |   initialize(begin, end, *(m.first), *(m.second));
      |   ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:550:69:   required from here
  550 |     markov_chain<size_t> ch(depth_values.begin(), depth_values.end());
      |                                                                     ^
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of 'constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator<vector<long int>*, vector<vector<long int> > >]', declared with attribute 'nodiscard' [-Wunused-result]
  114 |   for (; it != rend(), vit != values.rend(); it++, vit++) {
      |          ~~~^~~~~~~~~
In file included from /usr/include/c++/14/string:48,
                 from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:7:
/usr/include/c++/14/bits/stl_iterator.h:455:5: note: declared here
  455 |     operator!=(const reverse_iterator<_Iterator>& __x,
      |     ^~~~~~~~
[ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/ExtendParameters.cpp
[ 42%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/InputStructures.cpp
[ 43%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o
/usr/bin/cc -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF':
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
  678 |         fread(buf, 1, 28, fp->file);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)':
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
   36 |   arma::set_stream_err1(null_ostream);
      |   ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /usr/include/armadillo:412,
                 from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12:
/usr/include/armadillo_bits/debug.hpp:83:1: note: declared here
   83 | set_stream_err1(const std::ostream&)
      | ^~~~~~~~~~~~~~~
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations]
   37 |   arma::set_stream_err2(null_ostream);
      |   ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/usr/include/armadillo_bits/debug.hpp:92:1: note: declared here
   92 | set_stream_err2(const std::ostream&)
      | ^~~~~~~~~~~~~~~
[ 45%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o
/usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvcutils.dir/IonVersion.cpp.o -MF CMakeFiles/tvcutils.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/IonVersion.cpp
[ 46%] Linking CXX executable tvcassembly
/usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1
[ 48%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o
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/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF':
/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result]
  678 |         fread(buf, 1, 28, fp->file);
      |         ^~~~~~~~~~~~~~~~~~~~~~~~~~~
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	cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12
make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu'
Running tests...
/usr/bin/ctest --force-new-ctest-process --verbose -j12
UpdateCTestConfiguration  from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl
UpdateCTestConfiguration  from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/DartConfiguration.tcl
Test project /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
Connected to MAKE jobserver
test 1
    Start 1: tvc_call

1: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/tvc
1: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu
1: Test timeout computed to be: 10000000
test 2
    Start 2: tvc_test_1_thread_sse_off

2: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/test1" "--output-vcf" "small_variants.vcf"
2: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu
2: Test timeout computed to be: 10000000
test 3
    Start 3: tvc_test_4_threads_sse_off_with_parameter_file

3: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/test2" "--output-vcf" "small_variants.vcf"
3: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu
3: Test timeout computed to be: 10000000
test 4
    Start 4: tvcutils_call

4: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/tvcutils
4: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu
4: Test timeout computed to be: 10000000
test 5
    Start 5: tvcutils_prepare_hotspots_call

5: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/tvcutils "prepare_hotspots"
5: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu
5: Test timeout computed to be: 10000000
test 6
    Start 6: tvcutils_validate_bed_call

6: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/tvcutils "validate_bed"
6: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu
6: Test timeout computed to be: 10000000
test 7
    Start 7: tvcutils_unify_vcf_call

7: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/tvcutils "unify_vcf"
7: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu
7: Test timeout computed to be: 10000000
test 8
    Start 8: tvcassembly_call

8: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu/tvcassembly
8: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu
8: Test timeout computed to be: 10000000
1: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
1: 
1: Usage: tvc [options]
1: 
1: General options:
1:   -h,--help                                         print this help message and exit
1:   -v,--version                                      print version and exit
1:   -n,--num-threads                      INT         number of worker threads [2]
1:   -N,--num-variants-per-thread          INT         worker thread batch size [500]
1:      --parameters-file                  FILE        json file with algorithm control parameters [optional]
1: 
1: Inputs:
1:   -r,--reference                        FILE        reference fasta file [required]
1:   -b,--input-bam                        FILE        bam file with mapped reads [required]
1:   -g,--sample-name                      STRING      sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample]
1:      --force-sample-name                STRING      force all read groups to have this sample name [off]
1:   -t,--target-file                      FILE        only process targets in this bed file [optional]
1:      --trim-ampliseq-primers            on/off      match reads to targets and trim the ends that reach outside them [off]
1:   -D,--downsample-to-coverage           INT         ?? [2000]
1:      --model-file                       FILE        HP recalibration model input file.
1:      --recal-model-hp-thres             INT         Lower threshold for HP recalibration.
1: 
1: Outputs:
1:   -O,--output-dir                       DIRECTORY   base directory for all output files [current dir]
1:   -o,--output-vcf                       FILE        vcf file with variant calling results [required]
1:      --suppress-reference-genotypes     on/off      write reference calls into the filtered variants vcf [on]
1:      --suppress-no-calls                on/off      write filtered variants into the filtered variants vcf [on]
1:      --suppress-nocall-genotypes        on/off      do not report a genotype for filtered variants [on]
1: 
1: Variant candidate generation (FreeBayes):
1:      --allow-snps                       on/off      allow generation of snp candidates [on]
1:      --allow-indels                     on/off      allow generation of indel candidates [on]
1:      --allow-mnps                       on/off      allow generation of mnp candidates [on]
1:      --allow-complex                    on/off      allow generation of block substitution candidates [off]
1:      --max-complex-gap                  INT         maximum number of reference alleles between two alternate alleles to allow merging of the alternate alleles [1]
1:   -m,--use-best-n-alleles               INT         maximum number of snp alleles [2]
1:   -M,--min-mapping-qv                   INT         do not use reads with mapping quality below this [4]
1:   -U,--read-snp-limit                   INT         do not use reads with number of snps above this [10]
1:   -z,--read-max-mismatch-fraction       FLOAT       do not use reads with fraction of mismatches above this [1.0]
1:      --gen-min-alt-allele-freq          FLOAT       minimum required alt allele frequency to generate a candidate [0.2]
1:      --gen-min-indel-alt-allele-freq    FLOAT       minimum required alt allele frequency to generate a homopolymer indel candidate [0.2]
1:      --gen-min-coverage                 INT         minimum required coverage to generate a candidate [6]
1: 
1: External variant candidates:
1:   -c,--input-vcf                        FILE        vcf.gz file (+.tbi) with additional candidate variant locations and alleles [optional]
1:      --process-input-positions-only     on/off      only generate candidates at locations from input-vcf [off]
1:      --use-input-allele-only            on/off      only consider provided alleles for locations in input-vcf [off]
1: 
1: Variant candidate scoring options:
1:      --min-delta-for-flow               FLOAT       minimum prediction delta for scoring flows [0.1]
1:      --max-flows-to-test                INT         maximum number of scoring flows [10]
1:      --outlier-probability              FLOAT       probability for outlier reads [0.01]
1:      --heavy-tailed                     INT         degrees of freedom in t-dist modeling signal residual heavy tail [3]
1:      --suppress-recalibration           on/off      Suppress homopolymer recalibration [on].
1:      --do-snp-realignment               on/off      Realign reads in the vicinity of candidate snp variants [on].
1:      --do-mnp-realignment               on/off      Realign reads in the vicinity of candidate mnp variants [do-snp-realignment].
1:      --realignment-threshold            FLOAT       Max. allowed fraction of reads where realignment causes an alignment change [1.0].
1: 
1: Advanced variant candidate scoring options:
1:      --use-sse-basecaller               on/off      Switch to use the vectorized version of the basecaller [off].
1:      --resolve-clipped-bases            on/off      If 'true', the basecaller is used to solve soft clipped bases [off].
1:      --prediction-precision             FLOAT       prior weight in bias estimator [30.0]
1:      --shift-likelihood-penalty         FLOAT       penalize log-likelihood for solutions involving large systematic bias [0.3]
1:      --minimum-sigma-prior              FLOAT       prior variance per data point, constant [0.085]
1:      --slope-sigma-prior                FLOAT       prior rate of increase of variance over minimum by signal [0.0084]
1:      --sigma-prior-weight               FLOAT       weight of prior estimate of variance compared to observations [1.0]
1:      --k-zero                           FLOAT       variance increase for adding systematic bias [3.0]
1:      --sse-relative-safety-level        FLOAT       dampen strand bias detection for SSE events for low coverage [0.025]
1:      --tune-sbias                       FLOAT       dampen strand bias detection for low coverage [0.01]
1:      --max-detail-level                 INT         number of evaluated frequencies for a given hypothesis, reduce for very high coverage, set to zero to disable this option [0]
1: 
1: Variant filtering:
1:   -k,--snp-min-coverage                 INT         filter out snps with total coverage below this [6]
1:   -C,--snp-min-cov-each-strand          INT         filter out snps with coverage on either strand below this [0]
1:   -B,--snp-min-variant-score            FLOAT       filter out snps with QUAL score below this [10.0]
1:   -s,--snp-strand-bias                  FLOAT       filter out snps with strand bias above this [0.95] given pval < snp-strand-bias-pval
1:      --snp-strand-bias-pval             FLOAT       filter out snps with pval below this [1.0] given strand bias > snp-strand-bias
1:   -A,--snp-min-allele-freq              FLOAT       minimum required alt allele frequency for non-reference snp calls [0.2]
1:      --mnp-min-coverage                 INT         filter out mnps with total coverage below this [snp-min-coverage]
1:      --mnp-min-cov-each-strand          INT         filter out mnps with coverage on either strand below this, [snp-min-cov-each-strand]
1:      --mnp-min-variant-score            FLOAT       filter out mnps with QUAL score below this [snp-min-variant-score]
1:      --mnp-strand-bias                  FLOAT       filter out mnps with strand bias above this [snp-strand-bias] given pval < mnp-strand-bias-pval
1:      --mnp-strand-bias-pval             FLOAT       filter out mnps with pval below this [snp-strand-bias-pval] given strand bias > mnp-strand-bias
1:      --mnp-min-allele-freq              FLOAT       minimum required alt allele frequency for non-reference mnp calls [snp-min-allele-freq]
1:      --indel-min-coverage               INT         filter out indels with total coverage below this [30]
1:      --indel-min-cov-each-strand        INT         filter out indels with coverage on either strand below this [1]
1:      --indel-min-variant-score          FLOAT       filter out indels with QUAL score below this [10.0]
1:   -S,--indel-strand-bias                FLOAT       filter out indels with strand bias above this [0.95] given pval < indel-strand-bias-pval
1:      --indel-strand-bias-pval           FLOAT       filter out indels with pval below this [1.0] given strand bias > indel-strand-bias
1:      --indel-min-allele-freq            FLOAT       minimum required alt allele frequency for non-reference indel call [0.2]
1:      --hotspot-min-coverage             INT         filter out hotspot variants with total coverage below this [6]
1:      --hotspot-min-cov-each-strand      INT         filter out hotspot variants with coverage on either strand below this [snp-min-cov-each-strand]
1:      --hotspot-min-variant-score        FLOAT       filter out hotspot variants with QUAL score below this [snp-min-variant-score]
1:      --hotspot-strand-bias              FLOAT       filter out hotspot variants with strand bias above this [0.95] given pval < hotspot-strand-bias-pval
1:      --hotspot-strand-bias-pval         FLOAT       filter out hotspot variants with pval below this [1.0] given strand bias > hotspot-strand-bias
1:   -H,--hotspot-min-allele-freq          FLOAT       minimum required alt allele frequency for non-reference hotspot variant call [0.2]
1:   -L,--hp-max-length                    INT         filter out indels in homopolymers above this [8]
1:   -e,--error-motifs                     FILE        table of systematic error motifs and their error rates [optional]
1:      --sse-prob-threshold               FLOAT       filter out variants in motifs with error rates above this [0.2]
1:      --min-ratio-reads-non-sse-strand   FLOAT       minimum required alt allele frequency for variants with error motifs on opposite strand [0.2]
1:   --indel-as-hpindel                    on/off      apply indel filters to non HP indels [off]
1: 
1: Position bias variant filtering:
1:      --use-position-bias                on/off      enable the position bias filter [off]
1:      --position-bias                    FLOAT       filter out variants with position bias relative to soft clip ends in reads > position-bias [0.75]
1:      --position-bias-pval               FLOAT       filter out if position bias above position-bias given pval < position-bias-pval [0.05]
1:      --position-bias-ref-fraction       FLOAT       skip position bias filter if (reference read count)/(reference + alt allele read count) <= to this [0.05]
1: 
1: Filters that depend on scoring across alleles:
1:      --data-quality-stringency          FLOAT       minimum mean log-likelihood delta per read [4.0]
1:      --read-rejection-threshold         FLOAT       filter variants where large numbers of reads are rejected as outliers [0.5]
1:      --filter-unusual-predictions       FLOAT       posterior log likelihood threshold for accepting bias estimate [0.3]
1:      --filter-deletion-predictions      FLOAT       check post-evaluation systematic bias in deletions; a high value like 100 effectively turns off this filter [100.0]
1:      --filter-insertion-predictions     FLOAT       check post-evaluation systematic bias in insertions; a high value like 100 effectively turns off this filter [100.0]
1: 
1:      --heal-snps                        on/off      suppress in/dels not participating in diploid variant genotypes if the genotype contains a SNP or MNP [on].
1: 
1: Debugging:
1:   -d,--debug                            INT         (0/1/2) display extra debug messages [0]
1:      --do-json-diagnostic               on/off      (devel) dump internal state to json file (uses much more time/memory/disk) [off]
1:      --postprocessed-bam                FILE        (devel) save tvc-processed reads to an (unsorted) BAM file [optional]
1:      --do-minimal-diagnostic            on/off      (devel) provide minimal read information for called variants [off]
1:      --override-limits                  on/off      (devel) disable limit-check on input parameters [off].
1: 
2: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
2: 
2: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf
2:                       hp-max-length =          8 (integer, builtin default)
2:                  sse-prob-threshold =        0.2 (double,  builtin default)
2:      min-ratio-reads-non-sse-strand =        0.2 (double,  builtin default)
2:           sse-relative-safety-level =      0.025 (double,  builtin default)
2:                  do-snp-realignment =       true (boolean, builtin default)
2:                  do-mnp-realignment =       true (boolean, builtin default)
2:               realignment-threshold =          1 (double,  builtin default)
2:                    indel-as-hpindel =      false (boolean, builtin default)
2:             data-quality-stringency =          4 (double,  builtin default)
2:            read-rejection-threshold =        0.5 (double,  builtin default)
2:                   use-position-bias =      false (boolean, builtin default)
2:          position-bias-ref-fraction =       0.05 (double,  builtin default)
2:                       position-bias =       0.75 (double,  builtin default)
2:                  position-bias-pval =       0.05 (double,  builtin default)
2:              downsample-to-coverage =       2000 (integer, builtin default)
2:                          tune-sbias =       0.01 (double,  builtin default)
2:        suppress-reference-genotypes =       true (boolean, builtin default)
2:           suppress-nocall-genotypes =       true (boolean, builtin default)
2:                   suppress-no-calls =       true (boolean, builtin default)
2:                           heal-snps =       true (boolean, builtin default)
2:             snp-min-cov-each-strand =          0 (integer, builtin default)
2:               snp-min-variant-score =         10 (double,  builtin default)
2:                 snp-min-allele-freq =        0.2 (double,  builtin default)
2:                    snp-min-coverage =          6 (integer, builtin default)
2:                     snp-strand-bias =       0.95 (double,  builtin default)
2:                snp-strand-bias-pval =          1 (double,  builtin default)
2:             mnp-min-cov-each-strand =          0 (integer, builtin default)
2:               mnp-min-variant-score =         10 (double,  builtin default)
2:                 mnp-min-allele-freq =        0.2 (double,  builtin default)
2:                    mnp-min-coverage =          6 (integer, builtin default)
2:                     mnp-strand-bias =       0.95 (double,  builtin default)
2:                mnp-strand-bias-pval =          1 (double,  builtin default)
2:           indel-min-cov-each-strand =          1 (integer, builtin default)
2:             indel-min-variant-score =         10 (double,  builtin default)
2:               indel-min-allele-freq =        0.2 (double,  builtin default)
2:                  indel-min-coverage =         15 (integer, builtin default)
2:                   indel-strand-bias =       0.85 (double,  builtin default)
2:              indel-strand-bias-pval =          1 (double,  builtin default)
2:         hotspot-min-cov-each-strand =          0 (integer, builtin default)
2:           hotspot-min-variant-score =         10 (double,  builtin default)
2:             hotspot-min-allele-freq =        0.2 (double,  builtin default)
2:                hotspot-min-coverage =          6 (integer, builtin default)
2:                 hotspot-strand-bias =       0.95 (double,  builtin default)
2:            hotspot-strand-bias-pval =          1 (double,  builtin default)
2:                   max-flows-to-test =         10 (integer, builtin default)
2:                  min-delta-for-flow =        0.1 (double,  builtin default)
2:                prediction-precision =         30 (double,  builtin default)
2:                 outlier-probability =       0.01 (double,  builtin default)
2:             germline-prior-strength =          0 (double,  builtin default)
2:                        heavy-tailed =          3 (integer, builtin default)
2:          filter-unusual-predictions =        0.3 (double,  builtin default)
2:              soft-clip-bias-checker =        0.1 (double,  builtin default)
2:         filter-deletion-predictions =        100 (double,  builtin default)
2:        filter-insertion-predictions =        100 (double,  builtin default)
2:                    max-detail-level =          0 (integer, builtin default)
2:            shift-likelihood-penalty =        0.3 (double,  builtin default)
2:                 minimum-sigma-prior =      0.085 (double,  builtin default)
2:                   slope-sigma-prior =     0.0084 (double,  builtin default)
2:                  sigma-prior-weight =          1 (double,  builtin default)
2:                              k-zero =          3 (double,  builtin default)
2:                         num-threads =          1 (integer, command line option)
2:             num-variants-per-thread =        250 (integer, builtin default)
2:                  use-sse-basecaller =      false (boolean, command line option)
2:                  do-json-diagnostic =      false (boolean, builtin default)
2:               do-minimal-diagnostic =      false (boolean, builtin default)
2:        process-input-positions-only =      false (boolean, builtin default)
2:              suppress-recalibration =       true (boolean, builtin default)
2:               resolve-clipped-bases =      false (boolean, builtin default)
2: prefix-exclude = 6
2:                        allow-indels =       true (boolean, builtin default)
2:                          allow-snps =       true (boolean, builtin default)
2:                          allow-mnps =       true (boolean, builtin default)
2:                       allow-complex =      false (boolean, builtin default)
2:                   left-align-indels =      false (boolean, builtin default)
2:                  use-best-n-alleles =          2 (integer, builtin default)
2:               use-input-allele-only =      false (boolean, builtin default)
2:                      min-mapping-qv =          4 (integer, builtin default)
2:                      read-snp-limit =         10 (integer, builtin default)
2:          read-max-mismatch-fraction =          1 (double,  builtin default)
2:                     max-complex-gap =          1 (integer, builtin default)
2:             gen-min-alt-allele-freq =        0.2 (double,  builtin default)
2:                    gen-min-coverage =          6 (integer, builtin default)
2:       gen-min-indel-alt-allele-freq =        0.2 (double,  builtin default)
2:                     override-limits =      false (boolean, builtin default)
2: Limit check parameter hp-max-length: lim. 1 <= 8? OK!
2: Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK!
2: Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter data-quality-stringency: lim. 0 <= 4? OK!
2: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK!
2: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK!
2: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK!
2: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK!
2: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK!
2: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK!
2: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK!
2: Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK!
2: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter snp-min-coverage: lim. 0 <= 6? OK!
2: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
2: Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK!
2: Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK!
2: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK!
2: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
2: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK!
2: Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK!
2: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter indel-min-coverage: lim. 0 <= 15? OK!
2: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK!
2: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK!
2: Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK!
2: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK!
2: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
2: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK!
2: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK!
2: Limit check parameter prediction-precision: lim. 0.1 <= 30? OK!
2: Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK!
2: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK!
2: Limit check parameter heavy-tailed: lim. 1 <= 3? OK!
2: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK!
2: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK!
2: Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK!
2: Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK!
2: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK!
2: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK!
2: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK!
2: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK!
2: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK!
2: Limit check parameter k-zero: lim. 0 <= 3? OK!
2: Limit check parameter num-threads: lim. 1 <= 1 <= lim. 128? OK!
2: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK!
2: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK!
2: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK!
2: Limit check parameter read-snp-limit: lim. 0 <= 10? OK!
2: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK!
2: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK!
2: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK!
2: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed
2: TargetsManager: 1 target(s)
2: TargetsManager: Trimming of AmpliSeq primers is enabled
2: SampleManager: Found 1 read group(s) and 1 sample(s).
2: SampleManager: Primary sample "85" (default) present in 1 read group(s)
2: TVC found a total of 1 different flow orders of max flow lengths: 500
2: Recalibration was detected from comment lines in bam file(s):
2: 1 unique blocks of recalibration info detected.
2: Loading systematic error contexts.
3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller
3: 
3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf
3:                       hp-max-length =          8 (integer, parameters json file)
3:                  sse-prob-threshold =          1 (double,  parameters json file)
3:      min-ratio-reads-non-sse-strand =        0.2 (double,  builtin default)
3:           sse-relative-safety-level =      0.025 (double,  builtin default)
3:                  do-snp-realignment =      false (boolean, parameters json file)
3:                  do-mnp-realignment =      false (boolean, parameters json file)
3:               realignment-threshold =          0 (double,  parameters json file)
3:                    indel-as-hpindel =      false (boolean, parameters json file)
3:             data-quality-stringency =         10 (double,  parameters json file)
3:            read-rejection-threshold =        0.5 (double,  builtin default)
3:                   use-position-bias =      false (boolean, parameters json file)
3:          position-bias-ref-fraction =       0.05 (double,  parameters json file)
3:                       position-bias =       0.75 (double,  parameters json file)
3:                  position-bias-pval =       0.05 (double,  parameters json file)
3:              downsample-to-coverage =       2000 (integer, parameters json file)
3:                          tune-sbias =       0.01 (double,  builtin default)
3:        suppress-reference-genotypes =       true (boolean, builtin default)
3:           suppress-nocall-genotypes =       true (boolean, builtin default)
3:                   suppress-no-calls =       true (boolean, builtin default)
3:                           heal-snps =       true (boolean, builtin default)
3:             snp-min-cov-each-strand =          4 (integer, parameters json file)
3:               snp-min-variant-score =          6 (double,  parameters json file)
3:                 snp-min-allele-freq =       0.02 (double,  parameters json file)
3:                    snp-min-coverage =        100 (integer, parameters json file)
3:                     snp-strand-bias =       0.95 (double,  parameters json file)
3:                snp-strand-bias-pval =       0.01 (double,  parameters json file)
3:             mnp-min-cov-each-strand =          4 (integer, parameters json file)
3:               mnp-min-variant-score =          6 (double,  parameters json file)
3:                 mnp-min-allele-freq =       0.02 (double,  parameters json file)
3:                    mnp-min-coverage =        100 (integer, parameters json file)
3:                     mnp-strand-bias =       0.95 (double,  parameters json file)
3:                mnp-strand-bias-pval =       0.01 (double,  parameters json file)
3:           indel-min-cov-each-strand =          4 (integer, parameters json file)
3:             indel-min-variant-score =          6 (double,  parameters json file)
3:               indel-min-allele-freq =       0.02 (double,  parameters json file)
3:                  indel-min-coverage =        100 (integer, parameters json file)
3:                   indel-strand-bias =        0.9 (double,  parameters json file)
3:              indel-strand-bias-pval =          1 (double,  parameters json file)
3:         hotspot-min-cov-each-strand =          4 (integer, parameters json file)
3:           hotspot-min-variant-score =          6 (double,  parameters json file)
3:             hotspot-min-allele-freq =       0.02 (double,  parameters json file)
3:                hotspot-min-coverage =        100 (integer, parameters json file)
3:                 hotspot-strand-bias =       0.95 (double,  parameters json file)
3:            hotspot-strand-bias-pval =       0.01 (double,  parameters json file)
3:                   max-flows-to-test =         10 (integer, builtin default)
3:                  min-delta-for-flow =        0.1 (double,  builtin default)
3:                prediction-precision =          1 (double,  parameters json file)
3:                 outlier-probability =      0.005 (double,  parameters json file)
3:             germline-prior-strength =          0 (double,  builtin default)
3:                        heavy-tailed =          3 (integer, parameters json file)
3:          filter-unusual-predictions =       0.12 (double,  parameters json file)
3:              soft-clip-bias-checker =        0.1 (double,  builtin default)
3:         filter-deletion-predictions =        0.2 (double,  parameters json file)
3:        filter-insertion-predictions =        0.2 (double,  parameters json file)
3:                    max-detail-level =          0 (integer, builtin default)
3:            shift-likelihood-penalty =        0.3 (double,  builtin default)
3:                 minimum-sigma-prior =      0.085 (double,  builtin default)
3:                   slope-sigma-prior =     0.0084 (double,  builtin default)
3:                  sigma-prior-weight =          1 (double,  builtin default)
3:                              k-zero =          3 (double,  builtin default)
3:                         num-threads =          4 (integer, command line option)
3:             num-variants-per-thread =        250 (integer, builtin default)
3:                  use-sse-basecaller =      false (boolean, command line option)
3:                  do-json-diagnostic =      false (boolean, builtin default)
3:               do-minimal-diagnostic =      false (boolean, builtin default)
3:        process-input-positions-only =      false (boolean, builtin default)
3:              suppress-recalibration =      false (boolean, parameters json file)
3:               resolve-clipped-bases =      false (boolean, builtin default)
3: prefix-exclude = 6
3:                        allow-indels =       true (boolean, parameters json file)
3:                          allow-snps =       true (boolean, parameters json file)
3:                          allow-mnps =       true (boolean, parameters json file)
3:                       allow-complex =      false (boolean, parameters json file)
3:                   left-align-indels =      false (boolean, builtin default)
3:                  use-best-n-alleles =          2 (integer, builtin default)
3:               use-input-allele-only =      false (boolean, builtin default)
3:                      min-mapping-qv =          4 (integer, parameters json file)
3:                      read-snp-limit =         10 (integer, parameters json file)
3:          read-max-mismatch-fraction =          1 (double,  parameters json file)
3:                     max-complex-gap =          1 (integer, builtin default)
3:             gen-min-alt-allele-freq =       0.01 (double,  parameters json file)
3:                    gen-min-coverage =          6 (integer, parameters json file)
3:       gen-min-indel-alt-allele-freq =       0.01 (double,  parameters json file)
3:                     override-limits =      false (boolean, builtin default)
3: Limit check parameter hp-max-length: lim. 1 <= 8? OK!
3: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK!
3: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK!
3: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK!
3: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK!
3: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK!
3: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK!
3: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK!
3: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK!
3: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK!
3: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK!
3: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK!
3: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK!
3: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK!
3: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK!
3: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK!
3: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
3: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK!
3: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK!
3: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK!
3: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK!
3: Limit check parameter mnp-min-coverage: lim. 0 <= 100? OK!
3: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
3: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK!
3: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK!
3: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK!
3: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK!
3: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK!
3: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= lim. 1? OK!
3: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK!
3: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 4? OK!
3: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK!
3: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK!
3: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? OK!
3: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK!
3: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK!
3: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK!
3: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK!
3: Limit check parameter prediction-precision: lim. 0.1 <= 1? OK!
3: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= lim. 1? OK!
3: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK!
3: Limit check parameter heavy-tailed: lim. 1 <= 3? OK!
3: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.12? OK!
3: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK!
3: Limit check parameter filter-deletion-predictions: lim. 0 <= 0.2? OK!
3: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? OK!
3: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK!
3: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK!
3: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK!
3: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK!
3: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK!
3: Limit check parameter k-zero: lim. 0 <= 3? OK!
3: Limit check parameter num-threads: lim. 1 <= 4 <= lim. 128? OK!
3: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK!
3: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK!
3: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK!
3: Limit check parameter read-snp-limit: lim. 0 <= 10? OK!
3: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK!
3: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK!
3: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK!
3: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK!
3: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed
3: TargetsManager: 1 target(s)
3: TargetsManager: Trimming of AmpliSeq primers is enabled
3: SampleManager: Found 1 read group(s) and 1 sample(s).
3: SampleManager: Primary sample "85" (default) present in 1 read group(s)
3: TVC found a total of 1 different flow orders of max flow lengths: 500
3: Recalibration was detected from comment lines in bam file(s):
3: 1 unique blocks of recalibration info detected.
3: Loading systematic error contexts.
4: 
4: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
4: 
4: Usage:   tvcutils <command> [options]
4: 
4: Commands:
4:          prepare_hotspots  Convert BED or VCF file into a valid hotspot file
4:          validate_bed      Validate targets or hotspots file
4:          unify_vcf         Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots)
4: 
5: 
5: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
5: 
5: Usage:   tvcutils prepare_hotspots [options]
5: 
5: General options:
5:   -b,--input-bed                 FILE       input is a hotspots BED file (either -b or -v required)
5:   -v,--input-vcf                 FILE       input is a hotspots VCF file (either -b or -v required)
5:   -d,--output-bed                FILE       output left-aligned hotspots in BED format [none]
5:   -o,--output-vcf                FILE       output is a hotspots VCF file. To be used as input to --hotspot-vcf argument of variant_caller_pipeline.py (recommended) [none]
5:   -r,--reference                 FILE       FASTA file containing reference genome (required)
5:   -a,--left-alignment            on/off     perform left-alignment of indels [off]
5:   -s,--allow-block-substitutions on/off     do not filter out block substitution hotspots [on]
5:   -u,--unmerged-bed              FILE       input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional)
5: 
6: 
6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
6: 
6: Usage:   tvcutils validate_bed [options]
6: 
6: Input selection options (must provide one):
6:      --target-regions-bed        FILE       input is a target regions BED file (required)
6:      --hotspots-bed              FILE       input is a hotspots BED file (required)
6: 
6: General options:
6:      --reference                 FILE       FASTA file containing reference genome (required)
6:      --validation-log            FILE       log file for user-readable warning/error messages [stdout]
6:      --meta-json                 FILE       save validation and file statistics to json file [none]
6:      --unmerged-detail-bed       FILE       output a valid unmerged BED. To be used as input to --primer-trim-bed argument of variant_caller_pipeline.py (recommended) [none]
6:      --unmerged-plain-bed        FILE       output a valid merged BED. To be used as input to --region-bed argument of variant_caller_pipeline.py (recommended) [none]
6:      --merged-detail-bed         FILE       output an (almost) valid bedDetail merged BED [none]
6:      --merged-plain-bed          FILE       output a valid plain merged BED [none]
6:      --effective-bed             FILE       output a valid effective BED [none]
6: 
7: Parameter novel-tvc-vcf is required and empty.
7: 
7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow.
7: 
7: Usage:   tvcutils unify_vcf [options]
7: 
7: General options:
7:   -t,--novel-tvc-vcf             FILE       small variants VCF file produced by TVC (required)
7:   -i,--novel-assembly-vcf        FILE       long indels VCF file produced by TVCASSEMBLY (optional)
7:   -a,--hotspot-annotation-vcf    FILE       hotspot annotations VCF file (optional)
7:   -a,--hotspot-annotation-vcf    FILE       hotspot annotations VCF file (optional)
7:   -f,--reference-fasta           FILE       FASTA file containing reference genome (required)
7:   -b,--target-file               FILE       target regions BED file (optional)
7:   -o,--output-vcf                FILE       output merged and annotated VCF or VCF.GZ file (required)
7:   -j,--tvc-metrics               FILE       JSON file with tvc metrics (optional)
7:   -d,--input-depth               FILE       output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok)
7:   -m,--min-depth                 INT        minimum coverage depth in GVCF output (optional)
7: 
8: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly
8: 
8: Usage: tvcassembly [options]
8: 
8: General options:
8:   -h,--help                                         print this help message and exit
8:   -v,--version                                      print version and exit
8:   -n,--num-threads                      INT         number of worker threads [2]
8:      --parameters-file                  FILE        json file with algorithm control parameters [optional]
8:   -r,--reference                        FILE        reference fasta file [required]
8:   -b,--input-bam                        FILE        bam file with mapped reads [required]
8:   -t,--target-file                      FILE        only process targets in this bed file [optional]
8:   -o,--output-vcf                       FILE        vcf file with variant calling results [required]
8:   -g,--sample-name                      STRING      sample for which variants are called (In case of input BAM files with multiple samples) [optional if there is only one sample]
8:      --force-sample-name                STRING      force all read groups to have this sample name [off]
8: 
8:      --kmer_len                         INT         (klen) Size of the smallest k-mer used in assembly [19].
8:      --min_var_count                    INT         (mincount) Minimum support for a variant to be evaluated [5].
8:      --short_suffix_match               INT         (ssm) Minimum sequence match on both sides of the variant [5].
8:      --min_indel_size                   INT         (mis) Minimum size indel reported by assembly [4].
8:      --max_hp_length                    INT         (maxhp) Variants containing HP larger than this are not reported [8].
8:      --min_var_freq                     FLOAT       (minfreq) Minimum frequency of the variant to be reported [0.15].
8:      --min_var_score                    FLOAT       (minscore) Minimum score of the variant to be reported [10].
8:      --relative_strand_bias             FLOAT       (stbias) Variants with strand bias above this are not reported [0.80].
8:      --output_mnv                       INT         (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0].
8: 
1/8 Test #1: tvc_call .........................................   Passed    0.16 sec
2/8 Test #4: tvcutils_call ....................................   Passed    0.11 sec
3/8 Test #5: tvcutils_prepare_hotspots_call ...................   Passed    0.09 sec
4/8 Test #6: tvcutils_validate_bed_call .......................   Passed    0.07 sec
5/8 Test #7: tvcutils_unify_vcf_call ..........................   Passed    0.06 sec
6/8 Test #8: tvcassembly_call .................................   Passed    0.04 sec
3: Loaded.
3: 
3: 
3: [tvc] Normal termination. Processing time: 1 seconds.
7/8 Test #3: tvc_test_4_threads_sse_off_with_parameter_file ...   Passed    0.85 sec
2: Loaded.
2: Recalibration model: suppressed
2: 
2: 
2: [tvc] Normal termination. Processing time: 2 seconds.
8/8 Test #2: tvc_test_1_thread_sse_off ........................   Passed    1.31 sec

100% tests passed, 0 tests failed out of 8

Total Test time (real) =   1.33 sec
make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install --destdir=debian/tvc/
	cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make  -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf
-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf
make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-aarch64-linux-gnu'
   dh_installdocs
   dh_installchangelogs
   dh_lintian
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvcutils debian/tvc/usr/bin/tvc were not linked against libdisorder.so.0 (they use none of the library's symbols)
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_arm64.deb'.
dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_arm64.deb'.
 dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_arm64.buildinfo
 dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_arm64.changes
dpkg-genchanges: info: binary-only upload (no source code included)
 dpkg-source --after-build .
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/4010158/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/4010158/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/4010158 and its subdirectories
I: Current time: Wed Feb 26 09:05:27 +14 2025
I: pbuilder-time-stamp: 1740510327