I: pbuilder: network access will be disabled during build I: Current time: Sun Apr 30 19:09:49 +14 2023 I: pbuilder-time-stamp: 1682831389 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-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 gpgv: Signature made Wed Sep 7 05:33:36 2022 +14 gpgv: using RSA key 2D65BC1EB9665A6E97F9730AB3F5945285219E1F gpgv: issuer "mdbilal@disroot.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc: no acceptable signature found 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/1180282/tmp/hooks/D01_modify_environment starting debug: Running on ionos1-amd64. 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 Apr 30 19:10 /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/1180282/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/1180282/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]="15" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.2.15(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' DIRSTACK=() DISTRIBUTION=bookworm EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=580994be2149478f94ff6edc74d075c3 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-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=1180282 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.6OIiMJTx/pbuilderrc_RQFB --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6OIiMJTx/b2 --logfile b2/build.log --extrapackages usrmerge tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' SUDO_GID=110 SUDO_UID=105 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://78.137.99.97:3128 I: uname -a Linux i-capture-the-hostname 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 GNU/Linux I: ls -l /bin total 5632 -rwxr-xr-x 1 root root 1265648 Apr 24 11:23 bash -rwxr-xr-x 3 root root 39224 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 28 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 39224 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 14568 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 44016 Sep 21 2022 cat -rwxr-xr-x 1 root root 68656 Sep 21 2022 chgrp -rwxr-xr-x 1 root root 64496 Sep 21 2022 chmod -rwxr-xr-x 1 root root 72752 Sep 21 2022 chown -rwxr-xr-x 1 root root 151152 Sep 21 2022 cp -rwxr-xr-x 1 root root 125640 Jan 6 03:20 dash -rwxr-xr-x 1 root root 121904 Sep 21 2022 date -rwxr-xr-x 1 root root 89240 Sep 21 2022 dd -rwxr-xr-x 1 root root 102200 Sep 21 2022 df -rwxr-xr-x 1 root root 151344 Sep 21 2022 dir -rwxr-xr-x 1 root root 88656 Mar 24 00:02 dmesg lrwxrwxrwx 1 root root 8 Dec 20 03:33 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 20 03:33 domainname -> hostname -rwxr-xr-x 1 root root 43856 Sep 21 2022 echo -rwxr-xr-x 1 root root 41 Jan 25 04:43 egrep -rwxr-xr-x 1 root root 35664 Sep 21 2022 false -rwxr-xr-x 1 root root 41 Jan 25 04:43 fgrep -rwxr-xr-x 1 root root 85600 Mar 24 00:02 findmnt -rwsr-xr-x 1 root root 35128 Mar 23 22:35 fusermount -rwxr-xr-x 1 root root 203152 Jan 25 04:43 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 98136 Apr 10 2022 gzip -rwxr-xr-x 1 root root 22680 Dec 20 03:33 hostname -rwxr-xr-x 1 root root 72824 Sep 21 2022 ln -rwxr-xr-x 1 root root 53024 Mar 24 02:40 login -rwxr-xr-x 1 root root 151344 Sep 21 2022 ls -rwxr-xr-x 1 root root 207168 Mar 24 00:02 lsblk -rwxr-xr-x 1 root root 97552 Sep 21 2022 mkdir -rwxr-xr-x 1 root root 72912 Sep 21 2022 mknod -rwxr-xr-x 1 root root 43952 Sep 21 2022 mktemp -rwxr-xr-x 1 root root 59712 Mar 24 00:02 more -rwsr-xr-x 1 root root 59704 Mar 24 00:02 mount -rwxr-xr-x 1 root root 18744 Mar 24 00:02 mountpoint -rwxr-xr-x 1 root root 142968 Sep 21 2022 mv lrwxrwxrwx 1 root root 8 Dec 20 03:33 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 20:25 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 43952 Sep 21 2022 pwd lrwxrwxrwx 1 root root 4 Apr 24 11:23 rbash -> bash -rwxr-xr-x 1 root root 52112 Sep 21 2022 readlink -rwxr-xr-x 1 root root 72752 Sep 21 2022 rm -rwxr-xr-x 1 root root 56240 Sep 21 2022 rmdir -rwxr-xr-x 1 root root 27560 Nov 3 06:31 run-parts -rwxr-xr-x 1 root root 126424 Jan 6 09:55 sed lrwxrwxrwx 1 root root 9 Apr 30 19:10 sh -> /bin/bash -rwxr-xr-x 1 root root 43888 Sep 21 2022 sleep -rwxr-xr-x 1 root root 85008 Sep 21 2022 stty -rwsr-xr-x 1 root root 72000 Mar 24 00:02 su -rwxr-xr-x 1 root root 39824 Sep 21 2022 sync -rwxr-xr-x 1 root root 531984 Apr 7 04:25 tar -rwxr-xr-x 1 root root 14520 Nov 3 06:31 tempfile -rwxr-xr-x 1 root root 109616 Sep 21 2022 touch -rwxr-xr-x 1 root root 35664 Sep 21 2022 true -rwxr-xr-x 1 root root 14568 Mar 23 22:35 ulockmgr_server -rwsr-xr-x 1 root root 35128 Mar 24 00:02 umount -rwxr-xr-x 1 root root 43888 Sep 21 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 151344 Sep 21 2022 vdir -rwxr-xr-x 1 root root 72024 Mar 24 00:02 wdctl lrwxrwxrwx 1 root root 8 Dec 20 03:33 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/1180282/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: amd64 Maintainer: Debian Pbuilder Team 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 ... 19596 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} 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} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13{a} libarmadillo-dev{a} libarmadillo11{a} libarpack2{a} libarpack2-dev{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas-dev{a} libblas3{a} libboost-math-dev{a} libboost-math1.74-dev{a} libboost-math1.74.0{a} libboost1.74-dev{a} libbrotli1{a} libcurl4{a} libcurl4-openssl-dev{a} libdebhelper-perl{a} libdisorder-dev{a} libdisorder0{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libicu72{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp25{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libsuperlu-dev{a} libsuperlu5{a} libsz2{a} libtool{a} libuchardet0{a} libuv1{a} libxml2{a} m4{a} man-db{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 libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx psmisc publicsuffix wget 0 packages upgraded, 87 newly installed, 0 to remove and 0 not upgraded. Need to get 61.0 MB of archives. After unpacking 357 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get: 2 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get: 3 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 4 http://deb.debian.org/debian bookworm/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get: 5 http://deb.debian.org/debian bookworm/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get: 6 http://deb.debian.org/debian bookworm/main amd64 file amd64 1:5.44-3 [42.5 kB] Get: 7 http://deb.debian.org/debian bookworm/main amd64 gettext-base amd64 0.21-12 [160 kB] Get: 8 http://deb.debian.org/debian bookworm/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get: 9 http://deb.debian.org/debian bookworm/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get: 10 http://deb.debian.org/debian bookworm/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get: 11 http://deb.debian.org/debian bookworm/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get: 12 http://deb.debian.org/debian bookworm/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get: 13 http://deb.debian.org/debian bookworm/main amd64 m4 amd64 1.4.19-3 [287 kB] Get: 14 http://deb.debian.org/debian bookworm/main amd64 autoconf all 2.71-3 [332 kB] Get: 15 http://deb.debian.org/debian bookworm/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian bookworm/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian bookworm/main amd64 autopoint all 0.21-12 [495 kB] Get: 18 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get: 19 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.2 [687 kB] Get: 20 http://deb.debian.org/debian bookworm/main amd64 libarchive13 amd64 3.6.2-1 [343 kB] Get: 21 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get: 22 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get: 23 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get: 24 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get: 25 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get: 26 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get: 27 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get: 28 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get: 29 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-9 [386 kB] Get: 30 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get: 31 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp25 amd64 1.9.5-4 [78.6 kB] Get: 32 http://deb.debian.org/debian bookworm/main amd64 librhash0 amd64 1.4.3-3 [134 kB] Get: 33 http://deb.debian.org/debian bookworm/main amd64 libuv1 amd64 1.44.2-1 [140 kB] Get: 34 http://deb.debian.org/debian bookworm/main amd64 cmake-data all 3.25.1-1 [2026 kB] Get: 35 http://deb.debian.org/debian bookworm/main amd64 cmake amd64 3.25.1-1 [8692 kB] Get: 36 http://deb.debian.org/debian bookworm/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 37 http://deb.debian.org/debian bookworm/main amd64 libtool all 2.4.7-5 [517 kB] Get: 38 http://deb.debian.org/debian bookworm/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 39 http://deb.debian.org/debian bookworm/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 40 http://deb.debian.org/debian bookworm/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get: 41 http://deb.debian.org/debian bookworm/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 42 http://deb.debian.org/debian bookworm/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 43 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get: 44 http://deb.debian.org/debian bookworm/main amd64 dwz amd64 0.15-1 [109 kB] Get: 45 http://deb.debian.org/debian bookworm/main amd64 gettext amd64 0.21-12 [1300 kB] Get: 46 http://deb.debian.org/debian bookworm/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 47 http://deb.debian.org/debian bookworm/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 48 http://deb.debian.org/debian bookworm/main amd64 debhelper all 13.11.4 [942 kB] Get: 49 http://deb.debian.org/debian bookworm/main amd64 hdf5-helpers amd64 1.10.8+repack1-1 [27.9 kB] Get: 50 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get: 51 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get: 52 http://deb.debian.org/debian bookworm/main amd64 libaec-dev amd64 1.0.6-1+b1 [19.9 kB] Get: 53 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get: 54 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get: 55 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get: 56 http://deb.debian.org/debian bookworm/main amd64 libarpack2 amd64 3.8.0-3 [102 kB] Get: 57 http://deb.debian.org/debian bookworm/main amd64 libsuperlu5 amd64 5.3.0+dfsg1-2+b1 [170 kB] Get: 58 http://deb.debian.org/debian bookworm/main amd64 libarmadillo11 amd64 1:11.4.2+dfsg-1 [98.9 kB] Get: 59 http://deb.debian.org/debian bookworm/main amd64 libblas-dev amd64 3.11.0-2 [158 kB] Get: 60 http://deb.debian.org/debian bookworm/main amd64 liblapack-dev amd64 3.11.0-2 [4631 kB] Get: 61 http://deb.debian.org/debian bookworm/main amd64 libarpack2-dev amd64 3.8.0-3 [116 kB] Get: 62 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get: 63 http://deb.debian.org/debian bookworm/main amd64 libhdf5-fortran-102 amd64 1.10.8+repack1-1 [93.3 kB] Get: 64 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get: 65 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-fortran-100 amd64 1.10.8+repack1-1 [44.5 kB] Get: 66 http://deb.debian.org/debian bookworm/main amd64 libhdf5-cpp-103-1 amd64 1.10.8+repack1-1 [128 kB] Get: 67 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-cpp-100 amd64 1.10.8+repack1-1 [25.5 kB] Get: 68 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get: 69 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get: 70 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-2 [290 kB] Get: 71 http://deb.debian.org/debian bookworm/main amd64 libjpeg-dev amd64 1:2.1.5-2 [71.8 kB] Get: 72 http://deb.debian.org/debian bookworm/main amd64 libcurl4-openssl-dev amd64 7.88.1-9 [487 kB] Get: 73 http://deb.debian.org/debian bookworm/main amd64 libssl-dev amd64 3.0.8-1 [2427 kB] Get: 74 http://deb.debian.org/debian bookworm/main amd64 libhdf5-dev amd64 1.10.8+repack1-1 [2615 kB] Get: 75 http://deb.debian.org/debian bookworm/main amd64 libsuperlu-dev amd64 5.3.0+dfsg1-2+b1 [22.4 kB] Get: 76 http://deb.debian.org/debian bookworm/main amd64 libarmadillo-dev amd64 1:11.4.2+dfsg-1 [403 kB] Get: 77 http://deb.debian.org/debian bookworm/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-4 [149 kB] Get: 78 http://deb.debian.org/debian bookworm/main amd64 libbamtools-dev amd64 2.5.2+dfsg-4 [214 kB] Get: 79 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-20 [9510 kB] Get: 80 http://deb.debian.org/debian bookworm/main amd64 libboost-math1.74.0 amd64 1.74.0+ds1-20 [490 kB] Get: 81 http://deb.debian.org/debian bookworm/main amd64 libboost-math1.74-dev amd64 1.74.0+ds1-20 [564 kB] Get: 82 http://deb.debian.org/debian bookworm/main amd64 libboost-math-dev amd64 1.74.0.3 [4532 B] Get: 83 http://deb.debian.org/debian bookworm/main amd64 libdisorder0 amd64 0.0.2+git20130809.8062ee1-4+b1 [4884 B] Get: 84 http://deb.debian.org/debian bookworm/main amd64 libdisorder-dev amd64 0.0.2+git20130809.8062ee1-4+b1 [4860 B] Get: 85 http://deb.debian.org/debian bookworm/main amd64 libjsoncpp-dev amd64 1.9.5-4 [26.4 kB] Get: 86 http://deb.debian.org/debian bookworm/main amd64 libsmithwaterman0 amd64 0.0+git20160702.2610e25-12+b1 [36.5 kB] Get: 87 http://deb.debian.org/debian bookworm/main amd64 libsmithwaterman-dev amd64 0.0+git20160702.2610e25-12+b1 [40.8 kB] Fetched 61.0 MB in 2s (30.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19596 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.2-3_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.2-3_amd64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.17+nmu1_all.deb ... 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Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../27-libssh2-1_1.10.0-3+b1_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:amd64. Preparing to unpack .../28-libcurl4_7.88.1-9_amd64.deb ... Unpacking libcurl4:amd64 (7.88.1-9) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../29-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package libjsoncpp25:amd64. Preparing to unpack .../30-libjsoncpp25_1.9.5-4_amd64.deb ... Unpacking libjsoncpp25:amd64 (1.9.5-4) ... Selecting previously unselected package librhash0:amd64. Preparing to unpack .../31-librhash0_1.4.3-3_amd64.deb ... Unpacking librhash0:amd64 (1.4.3-3) ... Selecting previously unselected package libuv1:amd64. Preparing to unpack .../32-libuv1_1.44.2-1_amd64.deb ... 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Unpacking libdisorder-dev:amd64 (0.0.2+git20130809.8062ee1-4+b1) ... Selecting previously unselected package libjsoncpp-dev:amd64. Preparing to unpack .../84-libjsoncpp-dev_1.9.5-4_amd64.deb ... Unpacking libjsoncpp-dev:amd64 (1.9.5-4) ... Selecting previously unselected package libsmithwaterman0:amd64. Preparing to unpack .../85-libsmithwaterman0_0.0+git20160702.2610e25-12+b1_amd64.deb ... Unpacking libsmithwaterman0:amd64 (0.0+git20160702.2610e25-12+b1) ... Selecting previously unselected package libsmithwaterman-dev:amd64. Preparing to unpack .../86-libsmithwaterman-dev_0.0+git20160702.2610e25-12+b1_amd64.deb ... Unpacking libsmithwaterman-dev:amd64 (0.0+git20160702.2610e25-12+b1) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libdisorder0:amd64 (0.0.2+git20130809.8062ee1-4+b1) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-20) ... Setting up libicu72:amd64 (72.1-3) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up hdf5-helpers (1.10.8+repack1-1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsmithwaterman0:amd64 (0.0+git20160702.2610e25-12+b1) ... Setting up libnghttp2-14:amd64 (1.52.0-1) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libaec0:amd64 (1.0.6-1+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libuv1:amd64 (1.44.2-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... 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Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... usrmerge is already the newest version (35). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: user script /srv/workspace/pbuilder/1180282/tmp/hooks/A99_set_merged_usr starting Re-configuring usrmerge... removed '/etc/unsupported-skip-usrmerge-conversion' The system has been successfully converted. I: user script /srv/workspace/pbuilder/1180282/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/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 dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_FIND_USE_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j15 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/depend make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/depend make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvc.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake --color= make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' cd /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make -f CMakeFiles/tvc.dir/build.make 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-I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -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/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/MiscUtil.cpp [ 38%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function 'ti_index_core': /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 40%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF': /build/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 41%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io 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-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping/VcfFormat.cpp [ 47%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads/ExtendedReadInfo.cpp [ 49%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ErrorMotifs.cpp [ 50%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/LocalContext.cpp [ 52%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/ClassifyVariant.cpp In file included from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19: /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain::optimal_path() [with T = long unsigned int]': /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:64:3: required from 'void markov_chain::initialize(_ForwardIterator, _ForwardIterator, T, T) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = long unsigned int]' /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:38:13: required from 'markov_chain::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = long unsigned int]' /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here /build/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 > >]', declared with attribute 'nodiscard' [-Wunused-result] 114 | for (; it != rend(), vit != values.rend(); it++, vit++) { | ~~~^~~~~~~~~ In file included from /usr/include/c++/12/string:47, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:7: /usr/include/c++/12/bits/stl_iterator.h:458:5: note: declared here 458 | operator!=(const reverse_iterator<_Iterator>& __x, | ^~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(std::ostream&)' is deprecated [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/armadillo:385, from /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:92:1: note: declared here 92 | set_stream_err1(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(std::ostream&)' is deprecated [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/armadillo_bits/debug.hpp:103:1: note: declared here 103 | set_stream_err2(std::ostream& user_stream) | ^~~~~~~~~~~~~~~ [ 53%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/SpliceVariantHypotheses.cpp [ 55%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/DecisionTreeData.cpp [ 56%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp [ 58%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HypothesisEvaluator.cpp [ 60%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller 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CMakeFiles/tvc.dir/external/vcflib/split.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 76%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp [ 78%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c: In function 'ti_index_core': /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c:336:42: warning: overflow in conversion from 'uint32_t' {aka 'unsigned int'} to 'int32_t' {aka 'int'} changes value from 'last_bin = 4294967295' to '-1' [-Woverflow] 336 | save_bin = save_tid = last_tid = last_bin = 0xffffffffu; | ^~~~~~~~ [ 80%] Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval 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/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c [ 81%] Building CXX object CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -MF CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o.d -o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src/AlleleParser.cpp /build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF': /build/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); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/PIDloop.cpp [ 84%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping 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-ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -MF CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o.d -o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration/LinearCalibrationModel.cpp [ 87%] Linking CXX executable tvcutils /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcutils.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -Wl,-z,relro -rdynamic CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/tvcutils.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/prepare_hotspots.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/validate_bed.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -o tvcutils -lbamtools -lz -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' [ 87%] Built target tvcutils [ 89%] Building CXX object CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools 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-I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/IonVersion.cpp.o -MF CMakeFiles/tvc.dir/IonVersion.cpp.o.d -o CMakeFiles/tvc.dir/IonVersion.cpp.o -c /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/IonVersion.cpp [ 98%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval 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/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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 test 1 Start 1: tvc_call 1: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc 1: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 1: Test timeout computed to be: 10000000 test 2 Start 2: tvc_test_1_thread_sse_on 2: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc "--input-bam" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 2: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 2: Test timeout computed to be: 10000000 test 3 Start 3: tvc_test_1_thread_sse_off 3: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc "--input-bam" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/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/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 3: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 3: Test timeout computed to be: 10000000 test 4 Start 4: tvc_test_4_threads_sse_on_with_parameter_file 4: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc "--input-bam" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 4: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 4: Test timeout computed to be: 10000000 test 5 Start 5: tvc_test_4_threads_sse_off_with_parameter_file 5: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvc "--input-bam" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/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/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 5: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 5: Test timeout computed to be: 10000000 test 6 Start 6: tvcutils_call 6: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcutils 6: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 6: Test timeout computed to be: 10000000 test 7 Start 7: tvcutils_prepare_hotspots_call 7: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcutils "prepare_hotspots" 7: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 7: Test timeout computed to be: 10000000 test 8 Start 8: tvcutils_validate_bed_call 8: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcutils "validate_bed" 8: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 8: Test timeout computed to be: 10000000 test 9 Start 9: tvcutils_unify_vcf_call 9: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcutils "unify_vcf" 9: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 9: Test timeout computed to be: 10000000 test 10 Start 10: tvcassembly_call 10: Test command: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu/tvcassembly 10: Working Directory: /build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu 10: 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 [on]. 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 = true (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/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, builtin default) 3: sse-prob-threshold = 0.2 (double, builtin default) 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 = true (boolean, builtin default) 3: do-mnp-realignment = true (boolean, builtin default) 3: realignment-threshold = 1 (double, builtin default) 3: indel-as-hpindel = false (boolean, builtin default) 3: data-quality-stringency = 4 (double, builtin default) 3: read-rejection-threshold = 0.5 (double, builtin default) 3: use-position-bias = false (boolean, builtin default) 3: position-bias-ref-fraction = 0.05 (double, builtin default) 3: position-bias = 0.75 (double, builtin default) 3: position-bias-pval = 0.05 (double, builtin default) 3: downsample-to-coverage = 2000 (integer, builtin default) 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 = 0 (integer, builtin default) 3: snp-min-variant-score = 10 (double, builtin default) 3: snp-min-allele-freq = 0.2 (double, builtin default) 3: snp-min-coverage = 6 (integer, builtin default) 3: snp-strand-bias = 0.95 (double, builtin default) 3: snp-strand-bias-pval = 1 (double, builtin default) 3: mnp-min-cov-each-strand = 0 (integer, builtin default) 3: mnp-min-variant-score = 10 (double, builtin default) 3: mnp-min-allele-freq = 0.2 (double, builtin default) 3: mnp-min-coverage = 6 (integer, builtin default) 3: mnp-strand-bias = 0.95 (double, builtin default) 3: mnp-strand-bias-pval = 1 (double, builtin default) 3: indel-min-cov-each-strand = 1 (integer, builtin default) 3: indel-min-variant-score = 10 (double, builtin default) 3: indel-min-allele-freq = 0.2 (double, builtin default) 3: indel-min-coverage = 15 (integer, builtin default) 3: indel-strand-bias = 0.85 (double, builtin default) 3: indel-strand-bias-pval = 1 (double, builtin default) 3: hotspot-min-cov-each-strand = 0 (integer, builtin default) 3: hotspot-min-variant-score = 10 (double, builtin default) 3: hotspot-min-allele-freq = 0.2 (double, builtin default) 3: hotspot-min-coverage = 6 (integer, builtin default) 3: hotspot-strand-bias = 0.95 (double, builtin default) 3: hotspot-strand-bias-pval = 1 (double, builtin default) 3: max-flows-to-test = 10 (integer, builtin default) 3: min-delta-for-flow = 0.1 (double, builtin default) 3: prediction-precision = 30 (double, builtin default) 3: outlier-probability = 0.01 (double, builtin default) 3: germline-prior-strength = 0 (double, builtin default) 3: heavy-tailed = 3 (integer, builtin default) 3: filter-unusual-predictions = 0.3 (double, builtin default) 3: soft-clip-bias-checker = 0.1 (double, builtin default) 3: filter-deletion-predictions = 100 (double, builtin default) 3: filter-insertion-predictions = 100 (double, builtin default) 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 = 1 (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 = true (boolean, builtin default) 3: resolve-clipped-bases = false (boolean, builtin default) 3: prefix-exclude = 6 3: allow-indels = true (boolean, builtin default) 3: allow-snps = true (boolean, builtin default) 3: allow-mnps = true (boolean, builtin default) 3: allow-complex = false (boolean, builtin default) 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, builtin default) 3: read-snp-limit = 10 (integer, builtin default) 3: read-max-mismatch-fraction = 1 (double, builtin default) 3: max-complex-gap = 1 (integer, builtin default) 3: gen-min-alt-allele-freq = 0.2 (double, builtin default) 3: gen-min-coverage = 6 (integer, builtin default) 3: gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) 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 <= 0.2 <= 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 <= 1 <= lim. 1? OK! 3: Limit check parameter data-quality-stringency: lim. 0 <= 4? 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 <= 0? OK! 3: Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! 3: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter snp-min-coverage: lim. 0 <= 6? 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 <= 1 <= lim. 1? OK! 3: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! 3: Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! 3: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter mnp-min-coverage: lim. 0 <= 6? 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 <= 1 <= lim. 1? OK! 3: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! 3: Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! 3: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! 3: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= 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 <= 0? OK! 3: Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! 3: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! 3: Limit check parameter hotspot-min-coverage: lim. 0 <= 6? 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 <= 1 <= 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 <= 30? OK! 3: Limit check parameter outlier-probability: lim. 0 <= 0.01 <= 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 <= 0.3? 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 <= 100? OK! 3: Limit check parameter filter-insertion-predictions: lim. 0 <= 100? 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 <= 1 <= 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 <= 0.2 <= 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 <= 0.2 <= lim. 1? OK! 3: TargetsManager: Loaded targets file /build/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: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 4: 4: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 4: hp-max-length = 8 (integer, parameters json file) 4: sse-prob-threshold = 1 (double, parameters json file) 4: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 4: sse-relative-safety-level = 0.025 (double, builtin default) 4: do-snp-realignment = false (boolean, parameters json file) 4: do-mnp-realignment = false (boolean, parameters json file) 4: realignment-threshold = 0 (double, parameters json file) 4: indel-as-hpindel = false (boolean, parameters json file) 4: data-quality-stringency = 10 (double, parameters json file) 4: read-rejection-threshold = 0.5 (double, builtin default) 4: use-position-bias = false (boolean, parameters json file) 4: position-bias-ref-fraction = 0.05 (double, parameters json file) 4: position-bias = 0.75 (double, parameters json file) 4: position-bias-pval = 0.05 (double, parameters json file) 4: downsample-to-coverage = 2000 (integer, parameters json file) 4: tune-sbias = 0.01 (double, builtin default) 4: suppress-reference-genotypes = true (boolean, builtin default) 4: suppress-nocall-genotypes = true (boolean, builtin default) 4: suppress-no-calls = true (boolean, builtin default) 4: heal-snps = true (boolean, builtin default) 4: snp-min-cov-each-strand = 4 (integer, parameters json file) 4: snp-min-variant-score = 6 (double, parameters json file) 4: snp-min-allele-freq = 0.02 (double, parameters json file) 4: snp-min-coverage = 100 (integer, parameters json file) 4: snp-strand-bias = 0.95 (double, parameters json file) 4: snp-strand-bias-pval = 0.01 (double, parameters json file) 4: mnp-min-cov-each-strand = 4 (integer, parameters json file) 4: mnp-min-variant-score = 6 (double, parameters json file) 4: mnp-min-allele-freq = 0.02 (double, parameters json file) 4: mnp-min-coverage = 100 (integer, parameters json file) 4: mnp-strand-bias = 0.95 (double, parameters json file) 4: mnp-strand-bias-pval = 0.01 (double, parameters json file) 4: indel-min-cov-each-strand = 4 (integer, parameters json file) 4: indel-min-variant-score = 6 (double, parameters json file) 4: indel-min-allele-freq = 0.02 (double, parameters json file) 4: indel-min-coverage = 100 (integer, parameters json file) 4: indel-strand-bias = 0.9 (double, parameters json file) 4: indel-strand-bias-pval = 1 (double, parameters json file) 4: hotspot-min-cov-each-strand = 4 (integer, parameters json file) 4: hotspot-min-variant-score = 6 (double, parameters json file) 4: hotspot-min-allele-freq = 0.02 (double, parameters json file) 4: hotspot-min-coverage = 100 (integer, parameters json file) 4: hotspot-strand-bias = 0.95 (double, parameters json file) 4: hotspot-strand-bias-pval = 0.01 (double, parameters json file) 4: max-flows-to-test = 10 (integer, builtin default) 4: min-delta-for-flow = 0.1 (double, builtin default) 4: prediction-precision = 1 (double, parameters json file) 4: outlier-probability = 0.005 (double, parameters json file) 4: germline-prior-strength = 0 (double, builtin default) 4: heavy-tailed = 3 (integer, parameters json file) 4: filter-unusual-predictions = 0.12 (double, parameters json file) 4: soft-clip-bias-checker = 0.1 (double, builtin default) 4: filter-deletion-predictions = 0.2 (double, parameters json file) 4: filter-insertion-predictions = 0.2 (double, parameters json file) 4: max-detail-level = 0 (integer, builtin default) 4: shift-likelihood-penalty = 0.3 (double, builtin default) 4: minimum-sigma-prior = 0.085 (double, builtin default) 4: slope-sigma-prior = 0.0084 (double, builtin default) 4: sigma-prior-weight = 1 (double, builtin default) 4: k-zero = 3 (double, builtin default) 4: num-threads = 4 (integer, command line option) 4: num-variants-per-thread = 250 (integer, builtin default) 4: use-sse-basecaller = true (boolean, command line option) 4: do-json-diagnostic = false (boolean, builtin default) 4: do-minimal-diagnostic = false (boolean, builtin default) 4: process-input-positions-only = false (boolean, builtin default) 4: suppress-recalibration = false (boolean, parameters json file) 4: resolve-clipped-bases = false (boolean, builtin default) 4: prefix-exclude = 6 4: allow-indels = true (boolean, parameters json file) 4: allow-snps = true (boolean, parameters json file) 4: allow-mnps = true (boolean, parameters json file) 4: allow-complex = false (boolean, parameters json file) 4: left-align-indels = false (boolean, builtin default) 4: use-best-n-alleles = 2 (integer, builtin default) 4: use-input-allele-only = false (boolean, builtin default) 4: min-mapping-qv = 4 (integer, parameters json file) 4: read-snp-limit = 10 (integer, parameters json file) 4: read-max-mismatch-fraction = 1 (double, parameters json file) 4: max-complex-gap = 1 (integer, builtin default) 4: gen-min-alt-allele-freq = 0.01 (double, parameters json file) 4: gen-min-coverage = 6 (integer, parameters json file) 4: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file) 4: override-limits = false (boolean, builtin default) 4: Limit check parameter hp-max-length: lim. 1 <= 8? OK! 4: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK! 4: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 4: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 4: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK! 4: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK! 4: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 4: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 4: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 4: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 4: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 4: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 4: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK! 4: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK! 4: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 4: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK! 4: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 4: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 4: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK! 4: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK! 4: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 4: Limit check parameter mnp-min-coverage: lim. 0 <= 100? OK! 4: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 4: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 4: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK! 4: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK! 4: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 4: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK! 4: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= lim. 1? OK! 4: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 4: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 4? OK! 4: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK! 4: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 4: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? OK! 4: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 4: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 4: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 4: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 4: Limit check parameter prediction-precision: lim. 0.1 <= 1? OK! 4: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= lim. 1? OK! 4: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 4: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 4: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.12? OK! 4: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 4: Limit check parameter filter-deletion-predictions: lim. 0 <= 0.2? OK! 4: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? OK! 4: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 4: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 4: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 4: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 4: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 4: Limit check parameter k-zero: lim. 0 <= 3? OK! 4: Limit check parameter num-threads: lim. 1 <= 4 <= lim. 128? OK! 4: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 4: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 4: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 4: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 4: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 4: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 4: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 4: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 4: TargetsManager: Loaded targets file /build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 4: TargetsManager: 1 target(s) 4: TargetsManager: Trimming of AmpliSeq primers is enabled 4: SampleManager: Found 1 read group(s) and 1 sample(s). 4: SampleManager: Primary sample "85" (default) present in 1 read group(s) 4: TVC found a total of 1 different flow orders of max flow lengths: 500 4: Recalibration was detected from comment lines in bam file(s): 4: 1 unique blocks of recalibration info detected. 4: Loading systematic error contexts. 5: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 5: 5: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 5: hp-max-length = 8 (integer, parameters json file) 5: sse-prob-threshold = 1 (double, parameters json file) 5: min-ratio-reads-non-sse-strand = 0.2 (double, builtin default) 5: sse-relative-safety-level = 0.025 (double, builtin default) 5: do-snp-realignment = false (boolean, parameters json file) 5: do-mnp-realignment = false (boolean, parameters json file) 5: realignment-threshold = 0 (double, parameters json file) 5: indel-as-hpindel = false (boolean, parameters json file) 5: data-quality-stringency = 10 (double, parameters json file) 5: read-rejection-threshold = 0.5 (double, builtin default) 5: use-position-bias = false (boolean, parameters json file) 5: position-bias-ref-fraction = 0.05 (double, parameters json file) 5: position-bias = 0.75 (double, parameters json file) 5: position-bias-pval = 0.05 (double, parameters json file) 5: downsample-to-coverage = 2000 (integer, parameters json file) 5: tune-sbias = 0.01 (double, builtin default) 5: suppress-reference-genotypes = true (boolean, builtin default) 5: suppress-nocall-genotypes = true (boolean, builtin default) 5: suppress-no-calls = true (boolean, builtin default) 5: heal-snps = true (boolean, builtin default) 5: snp-min-cov-each-strand = 4 (integer, parameters json file) 5: snp-min-variant-score = 6 (double, parameters json file) 5: snp-min-allele-freq = 0.02 (double, parameters json file) 5: snp-min-coverage = 100 (integer, parameters json file) 5: snp-strand-bias = 0.95 (double, parameters json file) 5: snp-strand-bias-pval = 0.01 (double, parameters json file) 5: mnp-min-cov-each-strand = 4 (integer, parameters json file) 5: mnp-min-variant-score = 6 (double, parameters json file) 5: mnp-min-allele-freq = 0.02 (double, parameters json file) 5: mnp-min-coverage = 100 (integer, parameters json file) 5: mnp-strand-bias = 0.95 (double, parameters json file) 5: mnp-strand-bias-pval = 0.01 (double, parameters json file) 5: indel-min-cov-each-strand = 4 (integer, parameters json file) 5: indel-min-variant-score = 6 (double, parameters json file) 5: indel-min-allele-freq = 0.02 (double, parameters json file) 5: indel-min-coverage = 100 (integer, parameters json file) 5: indel-strand-bias = 0.9 (double, parameters json file) 5: indel-strand-bias-pval = 1 (double, parameters json file) 5: hotspot-min-cov-each-strand = 4 (integer, parameters json file) 5: hotspot-min-variant-score = 6 (double, parameters json file) 5: hotspot-min-allele-freq = 0.02 (double, parameters json file) 5: hotspot-min-coverage = 100 (integer, parameters json file) 5: hotspot-strand-bias = 0.95 (double, parameters json file) 5: hotspot-strand-bias-pval = 0.01 (double, parameters json file) 5: max-flows-to-test = 10 (integer, builtin default) 5: min-delta-for-flow = 0.1 (double, builtin default) 5: prediction-precision = 1 (double, parameters json file) 5: outlier-probability = 0.005 (double, parameters json file) 5: germline-prior-strength = 0 (double, builtin default) 5: heavy-tailed = 3 (integer, parameters json file) 5: filter-unusual-predictions = 0.12 (double, parameters json file) 5: soft-clip-bias-checker = 0.1 (double, builtin default) 5: filter-deletion-predictions = 0.2 (double, parameters json file) 5: filter-insertion-predictions = 0.2 (double, parameters json file) 5: max-detail-level = 0 (integer, builtin default) 5: shift-likelihood-penalty = 0.3 (double, builtin default) 5: minimum-sigma-prior = 0.085 (double, builtin default) 5: slope-sigma-prior = 0.0084 (double, builtin default) 5: sigma-prior-weight = 1 (double, builtin default) 5: k-zero = 3 (double, builtin default) 5: num-threads = 4 (integer, command line option) 5: num-variants-per-thread = 250 (integer, builtin default) 5: use-sse-basecaller = false (boolean, command line option) 5: do-json-diagnostic = false (boolean, builtin default) 5: do-minimal-diagnostic = false (boolean, builtin default) 5: process-input-positions-only = false (boolean, builtin default) 5: suppress-recalibration = false (boolean, parameters json file) 5: resolve-clipped-bases = false (boolean, builtin default) 5: prefix-exclude = 6 5: allow-indels = true (boolean, parameters json file) 5: allow-snps = true (boolean, parameters json file) 5: allow-mnps = true (boolean, parameters json file) 5: allow-complex = false (boolean, parameters json file) 5: left-align-indels = false (boolean, builtin default) 5: use-best-n-alleles = 2 (integer, builtin default) 5: use-input-allele-only = false (boolean, builtin default) 5: min-mapping-qv = 4 (integer, parameters json file) 5: read-snp-limit = 10 (integer, parameters json file) 5: read-max-mismatch-fraction = 1 (double, parameters json file) 5: max-complex-gap = 1 (integer, builtin default) 5: gen-min-alt-allele-freq = 0.01 (double, parameters json file) 5: gen-min-coverage = 6 (integer, parameters json file) 5: gen-min-indel-alt-allele-freq = 0.01 (double, parameters json file) 5: override-limits = false (boolean, builtin default) 5: Limit check parameter hp-max-length: lim. 1 <= 8? OK! 5: Limit check parameter sse-prob-threshold: lim. 0 <= 1 <= lim. 1? OK! 5: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! 5: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! 5: Limit check parameter realignment-threshold: lim. 0 <= 0 <= lim. 1? OK! 5: Limit check parameter data-quality-stringency: lim. 0 <= 10? OK! 5: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! 5: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! 5: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! 5: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! 5: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! 5: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! 5: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 4? OK! 5: Limit check parameter snp-min-variant-score: lim. 0 <= 6? OK! 5: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 5: Limit check parameter snp-min-coverage: lim. 0 <= 100? OK! 5: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 5: Limit check parameter snp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 5: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 4? OK! 5: Limit check parameter mnp-min-variant-score: lim. 0 <= 6? OK! 5: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 5: Limit check parameter mnp-min-coverage: lim. 0 <= 100? OK! 5: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 5: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 5: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 4? OK! 5: Limit check parameter indel-min-variant-score: lim. 0 <= 6? OK! 5: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 5: Limit check parameter indel-min-coverage: lim. 0 <= 100? OK! 5: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.9 <= lim. 1? OK! 5: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! 5: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 4? OK! 5: Limit check parameter hotspot-min-variant-score: lim. 0 <= 6? OK! 5: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.02 <= lim. 1? OK! 5: Limit check parameter hotspot-min-coverage: lim. 0 <= 100? OK! 5: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! 5: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 0.01 <= lim. 1? OK! 5: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! 5: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! 5: Limit check parameter prediction-precision: lim. 0.1 <= 1? OK! 5: Limit check parameter outlier-probability: lim. 0 <= 0.005 <= lim. 1? OK! 5: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! 5: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! 5: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.12? OK! 5: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! 5: Limit check parameter filter-deletion-predictions: lim. 0 <= 0.2? OK! 5: Limit check parameter filter-insertion-predictions: lim. 0 <= 0.2? OK! 5: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! 5: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! 5: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! 5: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! 5: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! 5: Limit check parameter k-zero: lim. 0 <= 3? OK! 5: Limit check parameter num-threads: lim. 1 <= 4 <= lim. 128? OK! 5: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! 5: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! 5: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! 5: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! 5: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! 5: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 5: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! 5: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.01 <= lim. 1? OK! 5: TargetsManager: Loaded targets file /build/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 5: TargetsManager: 1 target(s) 5: TargetsManager: Trimming of AmpliSeq primers is enabled 5: SampleManager: Found 1 read group(s) and 1 sample(s). 5: SampleManager: Primary sample "85" (default) present in 1 read group(s) 5: TVC found a total of 1 different flow orders of max flow lengths: 500 5: Recalibration was detected from comment lines in bam file(s): 5: 1 unique blocks of recalibration info detected. 5: Loading systematic error contexts. 6: 6: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 6: 6: Usage: tvcutils [options] 6: 6: Commands: 6: prepare_hotspots Convert BED or VCF file into a valid hotspot file 6: validate_bed Validate targets or hotspots file 6: unify_vcf Unify variants and annotations from all sources (tvc,IndelAssembly,hotpots) 6: 7: 7: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 7: 7: Usage: tvcutils prepare_hotspots [options] 7: 7: General options: 7: -b,--input-bed FILE input is a hotspots BED file (either -b or -v required) 7: -v,--input-vcf FILE input is a hotspots VCF file (either -b or -v required) 7: -d,--output-bed FILE output left-aligned hotspots in BED format [none] 7: -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] 7: -r,--reference FILE FASTA file containing reference genome (required) 7: -a,--left-alignment on/off perform left-alignment of indels [off] 7: -s,--allow-block-substitutions on/off do not filter out block substitution hotspots [on] 7: -u,--unmerged-bed FILE input a target bed file to filter out hotspots that contain a junction of 2 amplicons (optional) 7: 8: 8: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 8: 8: Usage: tvcutils validate_bed [options] 8: 8: Input selection options (must provide one): 8: --target-regions-bed FILE input is a target regions BED file (required) 8: --hotspots-bed FILE input is a hotspots BED file (required) 8: 8: General options: 8: --reference FILE FASTA file containing reference genome (required) 8: --validation-log FILE log file for user-readable warning/error messages [stdout] 8: --meta-json FILE save validation and file statistics to json file [none] 8: --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] 8: --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] 8: --merged-detail-bed FILE output an (almost) valid bedDetail merged BED [none] 8: --merged-plain-bed FILE output a valid plain merged BED [none] 8: --effective-bed FILE output a valid effective BED [none] 8: 9: Parameter novel-tvc-vcf is required and empty. 9: 9: tvcutils 5.0-3 (e975447-9fa85fb) - Miscellaneous tools used by Torrent Variant Caller plugin and workflow. 9: 9: Usage: tvcutils unify_vcf [options] 9: 9: General options: 9: -t,--novel-tvc-vcf FILE small variants VCF file produced by TVC (required) 9: -i,--novel-assembly-vcf FILE long indels VCF file produced by TVCASSEMBLY (optional) 9: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) 9: -a,--hotspot-annotation-vcf FILE hotspot annotations VCF file (optional) 9: -f,--reference-fasta FILE FASTA file containing reference genome (required) 9: -b,--target-file FILE target regions BED file (optional) 9: -o,--output-vcf FILE output merged and annotated VCF or VCF.GZ file (required) 9: -j,--tvc-metrics FILE JSON file with tvc metrics (optional) 9: -d,--input-depth FILE output of samtools depth. if provided, will cause generation of gvcf (optional, stdin ok) 9: -m,--min-depth INT minimum coverage depth in GVCF output (optional) 9: 10: tvcassembly 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller - Long Indel Assembly 10: 10: Usage: tvcassembly [options] 10: 10: General options: 10: -h,--help print this help message and exit 10: -v,--version print version and exit 10: -n,--num-threads INT number of worker threads [2] 10: --parameters-file FILE json file with algorithm control parameters [optional] 10: -r,--reference FILE reference fasta file [required] 10: -b,--input-bam FILE bam file with mapped reads [required] 10: -t,--target-file FILE only process targets in this bed file [optional] 10: -o,--output-vcf FILE vcf file with variant calling results [required] 10: -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] 10: --force-sample-name STRING force all read groups to have this sample name [off] 10: 10: --kmer_len INT (klen) Size of the smallest k-mer used in assembly [19]. 10: --min_var_count INT (mincount) Minimum support for a variant to be evaluated [5]. 10: --short_suffix_match INT (ssm) Minimum sequence match on both sides of the variant [5]. 10: --min_indel_size INT (mis) Minimum size indel reported by assembly [4]. 10: --max_hp_length INT (maxhp) Variants containing HP larger than this are not reported [8]. 10: --min_var_freq FLOAT (minfreq) Minimum frequency of the variant to be reported [0.15]. 10: --min_var_score FLOAT (minscore) Minimum score of the variant to be reported [10]. 10: --relative_strand_bias FLOAT (stbias) Variants with strand bias above this are not reported [0.80]. 10: --output_mnv INT (mnv) Output multi-nucleotide variants assembled in a region with multiple adjacent variants [0]. 10: 1/10 Test #1: tvc_call ......................................... Passed 0.19 sec 2/10 Test #6: tvcutils_call .................................... Passed 0.09 sec 3/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.08 sec 4/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.06 sec 5/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.05 sec 6/10 Test #10: tvcassembly_call ................................. Passed 0.03 sec 3: Loaded. 2: Loaded. 4: Loaded. 3: Recalibration model: suppressed 3: 3: 3: [tvc] Normal termination. Processing time: 2 seconds. 5: Loaded. 2: Recalibration model: suppressed 2: 2: 2: [tvc] Normal termination. Processing time: 3 seconds. 7/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 2.90 sec 5: 5: 5: [tvc] Normal termination. Processing time: 3 seconds. 4: 4: 4: [tvc] Normal termination. Processing time: 3 seconds. 8/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 3.30 sec 9/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 3.28 sec 10/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 3.79 sec 100% tests passed, 0 tests failed out of 10 Total Test time (real) = 3.85 sec make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ cd obj-x86_64-linux-gnu && make -j15 install DESTDIR=/build/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf make[1]: Leaving directory '/build/tvc-5.0.3+git20151221.80e144e+dfsg/obj-x86_64-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: 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-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_amd64.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_amd64.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_amd64.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_amd64.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/1180282/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/1180282/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/1180282 and its subdirectories I: Current time: Sun Apr 30 19:14:36 +14 2023 I: pbuilder-time-stamp: 1682831676