Running as unit: rb-build-i386_11-33961.service ==================================================================================== Fri Nov 22 16:37:59 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_i386_11) on jenkins, called using "ionos6-i386 ionos2-i386" as arguments. Fri Nov 22 16:37:59 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-YlVlQqkR" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 16:37:59 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos6-i386.debian.net is marked as down. Fri Nov 22 16:37:59 UTC 2024 - checking via ssh if ionos6-i386.debian.net is up. removed '/tmp/read-only-fs-test-13zD1M' Fri Nov 22 16:38:00 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos2-i386.debian.net is marked as down. Fri Nov 22 16:38:00 UTC 2024 - checking via ssh if ionos2-i386.debian.net is up. removed '/tmp/read-only-fs-test-XfuR73' ok, let's check if tvc is building anywhere yet… ok, tvc is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of tvc in trixie on i386 on jenkins now. 1st build will be done on ionos6-i386.debian.net. 2nd build will be done on ionos2-i386.debian.net. ============================================================================= Fri Nov 22 16:38:07 UTC 2024 I: starting to build tvc/trixie/i386 on jenkins on '2024-11-22 16:37' Fri Nov 22 16:38:07 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_11/33961/console.log 1732293487 i386 trixie tvc Fri Nov 22 16:38:07 UTC 2024 I: Downloading source for trixie/tvc=5.0.3+git20151221.80e144e+dfsg-5 --2024-11-22 16:38:07-- http://deb.debian.org/debian/pool/main/t/tvc/tvc_5.0.3%2bgit20151221.80e144e%2bdfsg-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2227 (2.2K) [text/prs.lines.tag] Saving to: ‘tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc’ 0K .. 100% 311M=0s 2024-11-22 16:38:07 (311 MB/s) - ‘tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc’ saved [2227/2227] --2024-11-22 16:38:07-- http://deb.debian.org/debian/pool/main/t/tvc/tvc_5.0.3%2bgit20151221.80e144e%2bdfsg-5.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2227 (2.2K) [text/prs.lines.tag] Saving to: ‘tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc’ 0K .. 100% 311M=0s 2024-11-22 16:38:07 (311 MB/s) - ‘tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc’ saved [2227/2227] Fri Nov 22 16:38:07 UTC 2024 I: tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: tvc Binary: tvc Architecture: any Version: 5.0.3+git20151221.80e144e+dfsg-5 Maintainer: Debian Med Packaging Team Uploaders: Dominique Belhachemi , Andreas Tille Homepage: http://ioncommunity.thermofisher.com Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/tvc Vcs-Git: https://salsa.debian.org/med-team/tvc.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), cmake, libbamtools-dev, libjsoncpp-dev, libarmadillo-dev, libboost-math-dev, libsmithwaterman-dev Package-List: tvc deb science optional arch=any Checksums-Sha1: cd0223b1b1c96a2cc5a25fbc64e4e36a00347788 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 7d0306db9bc6dc0e7cd4dede9e0a4fc26451cb66 9800 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz Checksums-Sha256: 3339f118d2fe983bc028630d5bf5238b6e91b70a85e8046a742588a6c342740c 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz ea878d69c94a1606583404cf23717d6a1dcc537bc4e6bd2c559ad2650939a52f 9800 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz Files: 68b468ca5054fb3260ad9de40131b632 744668 tvc_5.0.3+git20151221.80e144e+dfsg.orig.tar.xz 57be1c85cdcb34a4bc11e0493cbe5570 9800 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEELWW8HrlmWm6X+XMKs/WUUoUhnh8FAmMXaFAUHG1kYmlsYWxA ZGlzcm9vdC5vcmcACgkQs/WUUoUhnh+ysRAAiyxZr7pHEECCI+zBkWyVyHtCbKXV 92OCJejyYySi8hxtO5sWWmzAOItLKK2myc5v9tT7KcWHMqXVI+bpcODJQrEuc4r2 flZVmncIMhbf3jQ74V7acpHAg3H5bfL9MaOIU/oSv/TWHhze3hUqbO4ve+YfQ/Se tS6PZ2OPU/9aMwB/LrHZ2iVIoVg4pqZGuJvnuaREY2h0hEeqvyia4NP/YMyF3GiJ AAG3Q6EEH02jXuWOMIJzeeXQy34gYo7+eXleJWWsyAD44kXZG5SviIAkiz+g3iju PxxpPc5Uc9I2IiYK7eszn8Lo50RHh96V2dnt/h2y0D9An2po+T4nmqrVnZgtUwWt Vu+F7drjYwvxle7LMzDO91e7Q/StoFpZ68wT5uM6vt/f7SVbynlBYkx5WmzzXXU0 clsk8ULkNjHRun8W7BD90q0aRIKzYXF/fgmNod+F6cUqFEnoWSeBV1ffJfmqWcsA fGlAl8Zbxp218ARhEI5ChBuJafF3X7qshr2kMmst6L4ANeMmuJSCMfGToSsr7IyF ucGnYuJSaM6TiGFDpEMeQ8K2SmXJIQpJmZLrrKSgogRVCVTbEn6aJMvx2CcPZ3K9 DEG7/a98g0c2pscQuOtOxHCpQhf7IhR3HN3JDiDgWWngNa/TwM5AlLD+gSF9ZvsP 28/UEK2eq2cT8P4= =PDPe -----END PGP SIGNATURE----- Fri Nov 22 16:38:07 UTC 2024 I: Checking whether the package is not for us Fri Nov 22 16:38:07 UTC 2024 I: Starting 1st build on remote node ionos6-i386.debian.net. Fri Nov 22 16:38:07 UTC 2024 I: Preparing to do remote build '1' on ionos6-i386.debian.net. Fri Nov 22 16:38:07 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos6-i386.debian.net is marked as down. Fri Nov 22 16:38:07 UTC 2024 - checking via ssh if ionos6-i386.debian.net is up. removed '/tmp/read-only-fs-test-Sd17Az' ==================================================================================== Thu Dec 25 23:01:08 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos6-i386, called using "1 tvc trixie /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR 5.0.3+git20151221.80e144e+dfsg-5" as arguments. Thu Dec 25 23:01:08 UTC 2025 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-UOjeHOWO" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Thu Dec 25 23:01:08 UTC 2025 I: Downloading source for trixie/tvc=5.0.3+git20151221.80e144e+dfsg-5 Reading package lists... NOTICE: 'tvc' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tvc.git Please use: git clone https://salsa.debian.org/med-team/tvc.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 757 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (dsc) [2227 B] Get:2 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (tar) [745 kB] Get:3 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (diff) [9800 B] Fetched 757 kB in 0s (12.8 MB/s) Download complete and in download only mode Reading package lists... NOTICE: 'tvc' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tvc.git Please use: git clone https://salsa.debian.org/med-team/tvc.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 757 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (dsc) [2227 B] Get:2 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (tar) [745 kB] Get:3 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (diff) [9800 B] Fetched 757 kB in 0s (12.8 MB/s) Download complete and in download only mode ============================================================================= Building tvc in trixie on i386 on ionos6-i386 now. Date: Fri Dec 26 00:01:11 CET 2025 Date UTC: Thu Dec 25 23:01:11 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 25 11:01:12 -12 2025 I: pbuilder-time-stamp: 1766703672 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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: using eatmydata during job 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 Tue Sep 6 15:33:36 2022 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/119334/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='a3f0ea36e7ed41d2bcec0502d6e4e926' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='119334' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/pbuilderrc_E8YS --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos6-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/119334/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: i386 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 ... 19956 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libarmadillo-dev; however: Package libarmadillo-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-math-dev; however: Package libboost-math-dev is not installed. pbuilder-satisfydepends-dummy depends on libsmithwaterman-dev; however: Package libsmithwaterman-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libarmadillo-dev{a} libarmadillo14{a} libarpack2-dev{a} libarpack2t64{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas-dev{a} libblas3{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdisorder-dev{a} libdisorder0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldap-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsuperlu-dev{a} libsuperlu6{a} libsuperlu7{a} libsz2{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 76.9 MB of archives. After unpacking 412 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.30.5-1 [2223 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 27 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.0-1 [392 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libjsoncpp26 i386 1.9.6-2 [90.0 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 librhash1 i386 1.4.5-1 [144 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 cmake i386 3.30.5-1 [12.5 MB] Get: 42 http://deb.debian.org/debian trixie/main i386 comerr-dev i386 2.1-1.47.1-1+b1 [55.3 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 hdf5-helpers i386 1.10.10+repack-4 [23.5 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libgssrpc4t64 i386 1.21.3-3 [63.1 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libkadm5clnt-mit12 i386 1.21.3-3 [43.2 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libkdb5-10t64 i386 1.21.3-3 [45.1 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libkadm5srv-mit12 i386 1.21.3-3 [57.0 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 krb5-multidev i386 1.21.3-3 [126 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libaec0 i386 1.1.3-1+b1 [25.0 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libsz2 i386 1.1.3-1+b1 [8128 B] Get: 63 http://deb.debian.org/debian trixie/main i386 libaec-dev i386 1.1.3-1+b1 [23.0 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3+b1 [143 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3+b1 [2196 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libarpack2t64 i386 3.9.1-1.1+b1 [101 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libsuperlu6 i386 6.0.1+dfsg1-1+b1 [172 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libarmadillo14 i386 1:14.0.1+dfsg-2 [107 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.0-3+b1 [155 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 liblapack-dev i386 3.12.0-3+b1 [4452 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libarpack2-dev i386 3.9.1-1.1+b1 [120 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libhdf5-103-1t64 i386 1.10.10+repack-4 [1186 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libhdf5-fortran-102t64 i386 1.10.10+repack-4 [98.1 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-100t64 i386 1.10.10+repack-4 [76.0 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-fortran-100t64 i386 1.10.10+repack-4 [41.9 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libhdf5-cpp-103-1t64 i386 1.10.10+repack-4 [137 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-cpp-100t64 i386 1.10.10+repack-4 [21.9 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo-dev i386 1:2.1.5-3+b1 [305 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libjpeg-dev i386 1:2.1.5-3+b1 [72.2 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libbrotli-dev i386 1.1.0-2+b6 [313 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libkrb5-dev i386 1.21.3-3 [15.7 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libldap-dev i386 2.5.18+dfsg-3+b1 [324 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-2+b2 [330 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libgmp-dev i386 2:6.3.0+dfsg-2+b2 [661 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libunbound8 i386 1.22.0-1 [632 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libgnutls-dane0t64 i386 3.8.8-2 [447 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libgnutls-openssl27t64 i386 3.8.8-2 [447 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libp11-kit-dev i386 0.25.5-2+b1 [208 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libtasn1-6-dev i386 4.19.0-3+b3 [102 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 nettle-dev i386 3.10-1+b1 [1334 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libgnutls28-dev i386 3.8.8-2 [1453 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.3.2-2 [2790 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libzstd-dev i386 1.5.6+dfsg-1+b1 [355 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libcurl4-openssl-dev i386 8.11.0-1 [520 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libhdf5-dev i386 1.10.10+repack-4 [2783 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libsuperlu7 i386 7.0.0+dfsg1-2 [175 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libsuperlu-dev i386 7.0.0+dfsg1-2 [21.9 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libarmadillo-dev i386 1:14.0.1+dfsg-2 [413 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libbamtools2.5.2 i386 2.5.2+dfsg-6+b1 [178 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libbamtools-dev i386 2.5.2+dfsg-6+b1 [242 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libboost1.83-dev i386 1.83.0-3.2+b1 [10.6 MB] Get: 114 http://deb.debian.org/debian trixie/main i386 libboost-math1.83.0 i386 1.83.0-3.2+b1 [433 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libboost-math1.83-dev i386 1.83.0-3.2+b1 [511 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libboost-math-dev i386 1.83.0.2+b2 [3800 B] Get: 117 http://deb.debian.org/debian trixie/main i386 libdisorder0 i386 0.0.2+git20130809.8062ee1-4+b2 [4860 B] Get: 118 http://deb.debian.org/debian trixie/main i386 libdisorder-dev i386 0.0.2+git20130809.8062ee1-4+b2 [4868 B] Get: 119 http://deb.debian.org/debian trixie/main i386 libjsoncpp-dev i386 1.9.6-2 [24.9 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libsmithwaterman0 i386 0.0+git20160702.2610e25-12+b2 [38.7 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libsmithwaterman-dev i386 0.0+git20160702.2610e25-12+b2 [43.4 kB] Fetched 76.9 MB in 1s (73.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (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 ... 19956 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-6_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-6_i386.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../007-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.2-11_i386.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../010-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../017-cmake-data_3.30.5-1_all.deb ... Unpacking cmake-data (3.30.5-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../018-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../019-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:i386. Preparing to unpack .../020-libarchive13t64_3.7.4-1.1_i386.deb ... Unpacking libarchive13t64:i386 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../021-libbrotli1_1.1.0-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b6) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../022-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../023-libcom-err2_1.47.1-1+b1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../024-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../025-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../026-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../027-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../028-libsasl2-modules-db_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../029-libsasl2-2_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../030-libldap-2.5-0_2.5.18+dfsg-3+b1_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../031-libnghttp2-14_1.64.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:i386. Preparing to unpack .../032-libpsl5t64_0.21.2-1.1+b1_i386.deb ... Unpacking libpsl5t64:i386 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../033-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:i386. Preparing to unpack .../034-libssh2-1t64_1.11.1-1_i386.deb ... Unpacking libssh2-1t64:i386 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:i386. Preparing to unpack .../035-libcurl4t64_8.11.0-1_i386.deb ... Unpacking libcurl4t64:i386 (8.11.0-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../036-libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package libjsoncpp26:i386. Preparing to unpack .../037-libjsoncpp26_1.9.6-2_i386.deb ... Unpacking libjsoncpp26:i386 (1.9.6-2) ... Selecting previously unselected package librhash1:i386. Preparing to unpack .../038-librhash1_1.4.5-1_i386.deb ... Unpacking librhash1:i386 (1.4.5-1) ... Selecting previously unselected package libuv1t64:i386. Preparing to unpack .../039-libuv1t64_1.48.0-7_i386.deb ... Unpacking libuv1t64:i386 (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.30.5-1_i386.deb ... Unpacking cmake (3.30.5-1) ... Selecting previously unselected package comerr-dev:i386. Preparing to unpack .../041-comerr-dev_2.1-1.47.1-1+b1_i386.deb ... Unpacking comerr-dev:i386 (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../046-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../047-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../048-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../049-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../050-gettext_0.22.5-2_i386.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. 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Setting up libaec0:i386 (1.1.3-1+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libpsl-dev:i386 (0.21.2-1.1+b1) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libunbound8:i386 (1.22.0-1) ... Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-2+b2) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-3+b1) ... Setting up libgnutls-dane0t64:i386 (3.8.8-2) ... Setting up libjpeg62-turbo-dev:i386 (1:2.1.5-3+b1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:i386 (1.9.6-2) ... Setting up libproc2-0:i386 (2:4.0.4-6) ... Setting up comerr-dev:i386 (2.1-1.47.1-1+b1) ... Setting up libssl-dev:i386 (3.3.2-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libdisorder-dev:i386 (0.0.2+git20130809.8062ee1-4+b2) ... Setting up libbamtools2.5.2:i386 (2.5.2+dfsg-6+b1) ... Setting up libidn2-dev:i386 (2.3.7-2+b1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ... Setting up libgfortran5:i386 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up cmake-data (3.30.5-1) ... Setting up librhash1:i386 (1.4.5-1) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libssh2-1t64:i386 (1.11.1-1) ... Setting up libboost-math1.83.0:i386 (1.83.0-3.2+b1) ... Setting up libtasn1-6-dev:i386 (4.19.0-3+b3) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/i386-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 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 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' -- Configuring done (1.3s) -- Generating done (0.0s) 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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu dh_auto_build cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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 -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/depend make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 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-I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/DiagnosticJSON.cpp In file included from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain::optimal_path() [with T = unsigned int]': /build/reproducible-path/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 = unsigned int]' 64 | optimal_path(); | ^~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:38:13: required from 'markov_chain::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = unsigned int]' 38 | initialize(begin, end, *(m.first), *(m.second)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here 550 | markov_chain ch(depth_values.begin(), depth_values.end()); | ^ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of 'constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >]', declared with attribute 'nodiscard' [-Wunused-result] 114 | for (; it != rend(), vit != values.rend(); it++, vit++) { | ~~~^~~~~~~~~ In file included from /usr/include/c++/14/string:48, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:7: /usr/include/c++/14/bits/stl_iterator.h:455:5: note: declared here 455 | operator!=(const reverse_iterator<_Iterator>& __x, | ^~~~~~~~ [ 61%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/BiasGenerator.cpp [ 63%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SigmaGenerator.cpp [ 64%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SkewGenerator.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 191 | fprintf(stdout, "ref.size()=%lu; ", ref.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 192 | fprintf(stdout, "var.size()=%lu; ", var.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:193:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 193 | fprintf(stdout, "both.size()=%lu; ", both.size()); | ~~^ ~~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u [ 66%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/PosteriorInference.cpp [ 67%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/ShortStack.cpp [ 69%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/StackEngine.cpp [ 70%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/CrossHypotheses.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/armadillo:411, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:83:1: note: declared here 83 | set_stream_err1(const std::ostream&) | ^~~~~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/armadillo_bits/debug.hpp:92:1: note: declared here 92 | set_stream_err2(const std::ostream&) | ^~~~~~~~~~~~~~~ [ 72%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util 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Building C object CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -MF CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o.d -o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF': 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/IonVersion.cpp [ 95%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/TreephaserSSE.cpp [ 96%] Linking CXX executable tvcassembly /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/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/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvcassembly.dir/Util/OptArgs.cpp.o CMakeFiles/tvcassembly.dir/Util/Utils.cpp.o CMakeFiles/tvcassembly.dir/IonVersion.cpp.o -o tvcassembly -lbamtools -lz -lpthread -ljsoncpp make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 96%] Built target tvcassembly [ 98%] Linking CXX executable tvc /usr/bin/cmake -E cmake_link_script CMakeFiles/tvc.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/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/tvc.dir/VariantCaller/VariantCaller.cpp.o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o "CMakeFiles/tvc.dir/file-io/ion_util.c.o" "CMakeFiles/tvc.dir/file-io/ion_error.c.o" CMakeFiles/tvc.dir/IonVersion.cpp.o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 98%] Built target tvc [100%] 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/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [100%] Built target tvcutils make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' dh_auto_test cd obj-i686-linux-gnu && make -j22 test ARGS\+=--verbose ARGS\+=-j22 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j22 UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc 1: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 1: Test timeout computed to be: 10000000 test 2 Start 2: tvc_test_1_thread_sse_on 2: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 2: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 2: Test timeout computed to be: 10000000 test 3 Start 3: tvc_test_1_thread_sse_off 3: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 3: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 4: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 5: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 5: Test timeout computed to be: 10000000 test 6 Start 6: tvcutils_call 6: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils 6: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 6: Test timeout computed to be: 10000000 test 7 Start 7: tvcutils_prepare_hotspots_call 7: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "prepare_hotspots" 7: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 7: Test timeout computed to be: 10000000 test 8 Start 8: tvcutils_validate_bed_call 8: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "validate_bed" 8: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 8: Test timeout computed to be: 10000000 test 9 Start 9: tvcutils_unify_vcf_call 9: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "unify_vcf" 9: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 9: Test timeout computed to be: 10000000 test 10 Start 10: tvcassembly_call 10: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcassembly 10: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 2: TargetsManager: 1 target(s) 2: TargetsManager: Trimming of AmpliSeq primers is enabled 2: SampleManager: Found 1 read group(s) and 1 sample(s). 2: SampleManager: Primary sample "85" (default) present in 1 read group(s) 2: TVC found a total of 1 different flow orders of max flow lengths: 500 2: Recalibration was detected from comment lines in bam file(s): 2: 1 unique blocks of recalibration info detected. 2: Loading systematic error contexts. 3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 3: 3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 3: hp-max-length = 8 (integer, 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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 3: TargetsManager: 1 target(s) 3: TargetsManager: Trimming of AmpliSeq primers is enabled 3: SampleManager: Found 1 read group(s) and 1 sample(s). 3: SampleManager: Primary sample "85" (default) present in 1 read group(s) 3: TVC found a total of 1 different flow orders of max flow lengths: 500 3: Recalibration was detected from comment lines in bam file(s): 3: 1 unique blocks of recalibration info detected. 3: Loading systematic error contexts. 4: 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/reproducible-path/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/reproducible-path/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 0.11 sec 3/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.09 sec 4/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.08 sec 5/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.06 sec 6/10 Test #10: tvcassembly_call ................................. Passed 0.05 sec 5: Loaded. 2: Loaded. 3: Loaded. 4: Loaded. 2: Recalibration model: suppressed 2: 2: 2: [tvc] Normal termination. Processing time: 1 seconds. 5: 5: 5: [tvc] Normal termination. Processing time: 1 seconds. 3: Recalibration model: suppressed 3: 3: 3: [tvc] Normal termination. Processing time: 1 seconds. 7/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 1.54 sec 8/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.49 sec 9/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 1.60 sec 4: 4: 4: [tvc] Normal termination. Processing time: 1 seconds. 10/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 1.81 sec 100% tests passed, 0 tests failed out of 10 Total Test time (real) = 1.88 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ cd obj-i686-linux-gnu && make -j22 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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_i386.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.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: 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/119334 and its subdirectories I: Current time: Thu Dec 25 11:03:25 -12 2025 I: pbuilder-time-stamp: 1766703805 Thu Dec 25 23:03:25 UTC 2025 I: Signing ./b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo as tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc Thu Dec 25 23:03:26 UTC 2025 I: Signed ./b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo as ./b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc Thu Dec 25 23:03:26 UTC 2025 - build #1 for tvc/trixie/i386 on ionos6-i386 done. Starting cleanup. All cleanup done. Thu Dec 25 23:03:26 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-UOjeHOWO, removing. /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR: total 16 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 16:40 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 16:38 b2 -rw------- 1 jenkins jenkins 3420 Nov 22 16:38 rbuildlog.Kw0KWkO -rw-r--r-- 1 jenkins jenkins 2227 Sep 6 2022 tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b1: total 12788 -rw-r--r-- 1 jenkins jenkins 260879 Nov 22 16:40 build.log -rw-r--r-- 1 jenkins jenkins 11624408 Nov 22 16:40 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_i386.deb -rw-r--r-- 1 jenkins jenkins 9800 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2227 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc -rw-r--r-- 1 jenkins jenkins 8420 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 9302 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1747 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes -rw-r--r-- 1 jenkins jenkins 1158148 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb -rw-r--r-- 1 jenkins jenkins 1599 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b2: total 0 Fri Nov 22 16:40:28 UTC 2024 I: Deleting $TMPDIR on ionos6-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Dec 25 11:01:12 -12 2025 I: pbuilder-time-stamp: 1766703672 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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: using eatmydata during job 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 Tue Sep 6 15:33:36 2022 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/119334/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='a3f0ea36e7ed41d2bcec0502d6e4e926' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='119334' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/pbuilderrc_E8YS --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos6-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/119334/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: i386 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 ... 19956 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libarmadillo-dev; however: Package libarmadillo-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-math-dev; however: Package libboost-math-dev is not installed. pbuilder-satisfydepends-dummy depends on libsmithwaterman-dev; however: Package libsmithwaterman-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libarmadillo-dev{a} libarmadillo14{a} libarpack2-dev{a} libarpack2t64{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas-dev{a} libblas3{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdisorder-dev{a} libdisorder0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldap-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsuperlu-dev{a} libsuperlu6{a} libsuperlu7{a} libsz2{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 76.9 MB of archives. After unpacking 412 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.30.5-1 [2223 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 27 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.0-1 [392 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libjsoncpp26 i386 1.9.6-2 [90.0 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 librhash1 i386 1.4.5-1 [144 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 cmake i386 3.30.5-1 [12.5 MB] Get: 42 http://deb.debian.org/debian trixie/main i386 comerr-dev i386 2.1-1.47.1-1+b1 [55.3 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 hdf5-helpers i386 1.10.10+repack-4 [23.5 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libgssrpc4t64 i386 1.21.3-3 [63.1 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libkadm5clnt-mit12 i386 1.21.3-3 [43.2 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libkdb5-10t64 i386 1.21.3-3 [45.1 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libkadm5srv-mit12 i386 1.21.3-3 [57.0 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 krb5-multidev i386 1.21.3-3 [126 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libaec0 i386 1.1.3-1+b1 [25.0 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libsz2 i386 1.1.3-1+b1 [8128 B] Get: 63 http://deb.debian.org/debian trixie/main i386 libaec-dev i386 1.1.3-1+b1 [23.0 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3+b1 [143 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3+b1 [2196 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libarpack2t64 i386 3.9.1-1.1+b1 [101 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libsuperlu6 i386 6.0.1+dfsg1-1+b1 [172 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libarmadillo14 i386 1:14.0.1+dfsg-2 [107 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.0-3+b1 [155 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 liblapack-dev i386 3.12.0-3+b1 [4452 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libarpack2-dev i386 3.9.1-1.1+b1 [120 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libhdf5-103-1t64 i386 1.10.10+repack-4 [1186 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libhdf5-fortran-102t64 i386 1.10.10+repack-4 [98.1 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-100t64 i386 1.10.10+repack-4 [76.0 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-fortran-100t64 i386 1.10.10+repack-4 [41.9 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libhdf5-cpp-103-1t64 i386 1.10.10+repack-4 [137 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-cpp-100t64 i386 1.10.10+repack-4 [21.9 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo-dev i386 1:2.1.5-3+b1 [305 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libjpeg-dev i386 1:2.1.5-3+b1 [72.2 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libbrotli-dev i386 1.1.0-2+b6 [313 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libkrb5-dev i386 1.21.3-3 [15.7 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libldap-dev i386 2.5.18+dfsg-3+b1 [324 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-2+b2 [330 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libgmp-dev i386 2:6.3.0+dfsg-2+b2 [661 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libunbound8 i386 1.22.0-1 [632 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libgnutls-dane0t64 i386 3.8.8-2 [447 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libgnutls-openssl27t64 i386 3.8.8-2 [447 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libp11-kit-dev i386 0.25.5-2+b1 [208 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libtasn1-6-dev i386 4.19.0-3+b3 [102 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 nettle-dev i386 3.10-1+b1 [1334 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libgnutls28-dev i386 3.8.8-2 [1453 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.3.2-2 [2790 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libzstd-dev i386 1.5.6+dfsg-1+b1 [355 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libcurl4-openssl-dev i386 8.11.0-1 [520 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libhdf5-dev i386 1.10.10+repack-4 [2783 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libsuperlu7 i386 7.0.0+dfsg1-2 [175 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libsuperlu-dev i386 7.0.0+dfsg1-2 [21.9 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libarmadillo-dev i386 1:14.0.1+dfsg-2 [413 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libbamtools2.5.2 i386 2.5.2+dfsg-6+b1 [178 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libbamtools-dev i386 2.5.2+dfsg-6+b1 [242 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libboost1.83-dev i386 1.83.0-3.2+b1 [10.6 MB] Get: 114 http://deb.debian.org/debian trixie/main i386 libboost-math1.83.0 i386 1.83.0-3.2+b1 [433 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libboost-math1.83-dev i386 1.83.0-3.2+b1 [511 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libboost-math-dev i386 1.83.0.2+b2 [3800 B] Get: 117 http://deb.debian.org/debian trixie/main i386 libdisorder0 i386 0.0.2+git20130809.8062ee1-4+b2 [4860 B] Get: 118 http://deb.debian.org/debian trixie/main i386 libdisorder-dev i386 0.0.2+git20130809.8062ee1-4+b2 [4868 B] Get: 119 http://deb.debian.org/debian trixie/main i386 libjsoncpp-dev i386 1.9.6-2 [24.9 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libsmithwaterman0 i386 0.0+git20160702.2610e25-12+b2 [38.7 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libsmithwaterman-dev i386 0.0+git20160702.2610e25-12+b2 [43.4 kB] Fetched 76.9 MB in 1s (73.0 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (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 ... 19956 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-6_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-6_i386.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../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 i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/i386-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. 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'/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 1%] Building CXX object CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/DiagnosticJSON.cpp In file included from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain::optimal_path() [with T = unsigned int]': /build/reproducible-path/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 = unsigned int]' 64 | optimal_path(); | ^~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:38:13: required from 'markov_chain::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = unsigned int]' 38 | initialize(begin, end, *(m.first), *(m.second)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here 550 | markov_chain ch(depth_values.begin(), depth_values.end()); | ^ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of 'constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >]', declared with attribute 'nodiscard' [-Wunused-result] 114 | for (; it != rend(), vit != values.rend(); it++, vit++) { | ~~~^~~~~~~~~ In file included from /usr/include/c++/14/string:48, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:7: /usr/include/c++/14/bits/stl_iterator.h:455:5: note: declared here 455 | operator!=(const reverse_iterator<_Iterator>& __x, | ^~~~~~~~ [ 61%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/BiasGenerator.cpp [ 63%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SigmaGenerator.cpp [ 64%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/SkewGenerator.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 191 | fprintf(stdout, "ref.size()=%lu; ", ref.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 192 | fprintf(stdout, "var.size()=%lu; ", var.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:193:37: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 193 | fprintf(stdout, "both.size()=%lu; ", both.size()); | ~~^ ~~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u [ 66%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/PosteriorInference.cpp [ 67%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/ShortStack.cpp [ 69%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/StackEngine.cpp [ 70%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/CrossHypotheses.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/armadillo:411, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:83:1: note: declared here 83 | set_stream_err1(const std::ostream&) | ^~~~~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/armadillo_bits/debug.hpp:92:1: note: declared here 92 | set_stream_err2(const std::ostream&) | ^~~~~~~~~~~~~~~ [ 72%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp [ 73%] Building CXX object CMakeFiles/tvc.dir/external/vcflib/split.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/file-io/ion_error.c.o -MF CMakeFiles/tvc.dir/file-io/ion_error.c.o.d -o CMakeFiles/tvc.dir/file-io/ion_error.c.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_error.c [ 93%] Building CXX object CMakeFiles/tvc.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/IonVersion.cpp [ 95%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/TreephaserSSE.cpp [ 96%] Linking CXX executable tvcassembly /usr/bin/cmake -E cmake_link_script CMakeFiles/tvcassembly.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/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/tvcassembly.dir/VariantCaller/IndelAssembly/IndelAssembly.cpp.o CMakeFiles/tvcassembly.dir/VariantCaller/TargetsManager.cpp.o 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CMakeFiles/tvc.dir/Util/OptArgs.cpp.o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o "CMakeFiles/tvc.dir/file-io/ion_util.c.o" "CMakeFiles/tvc.dir/file-io/ion_error.c.o" CMakeFiles/tvc.dir/IonVersion.cpp.o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 98%] Built target tvc [100%] 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/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [100%] Built target tvcutils make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles 0 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Checking test dependency graph end test 1 Start 1: tvc_call 1: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc 1: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 1: Test timeout computed to be: 10000000 test 2 Start 2: tvc_test_1_thread_sse_on 2: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 2: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 2: Test timeout computed to be: 10000000 test 3 Start 3: tvc_test_1_thread_sse_off 3: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 3: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 4: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 5: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 5: Test timeout computed to be: 10000000 test 6 Start 6: tvcutils_call 6: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils 6: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 6: Test timeout computed to be: 10000000 test 7 Start 7: tvcutils_prepare_hotspots_call 7: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "prepare_hotspots" 7: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 7: Test timeout computed to be: 10000000 test 8 Start 8: tvcutils_validate_bed_call 8: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "validate_bed" 8: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 8: Test timeout computed to be: 10000000 test 9 Start 9: tvcutils_unify_vcf_call 9: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "unify_vcf" 9: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 9: Test timeout computed to be: 10000000 test 10 Start 10: tvcassembly_call 10: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcassembly 10: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 2: TargetsManager: 1 target(s) 2: TargetsManager: Trimming of AmpliSeq primers is enabled 2: SampleManager: Found 1 read group(s) and 1 sample(s). 2: SampleManager: Primary sample "85" (default) present in 1 read group(s) 2: TVC found a total of 1 different flow orders of max flow lengths: 500 2: Recalibration was detected from comment lines in bam file(s): 2: 1 unique blocks of recalibration info detected. 2: Loading systematic error contexts. 3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 3: 3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf 3: hp-max-length = 8 (integer, 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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 3: TargetsManager: 1 target(s) 3: TargetsManager: Trimming of AmpliSeq primers is enabled 3: SampleManager: Found 1 read group(s) and 1 sample(s). 3: SampleManager: Primary sample "85" (default) present in 1 read group(s) 3: TVC found a total of 1 different flow orders of max flow lengths: 500 3: Recalibration was detected from comment lines in bam file(s): 3: 1 unique blocks of recalibration info detected. 3: Loading systematic error contexts. 4: 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/reproducible-path/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/reproducible-path/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 0.11 sec 3/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.09 sec 4/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.08 sec 5/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.06 sec 6/10 Test #10: tvcassembly_call ................................. Passed 0.05 sec 5: Loaded. 2: Loaded. 3: Loaded. 4: Loaded. 2: Recalibration model: suppressed 2: 2: 2: [tvc] Normal termination. Processing time: 1 seconds. 5: 5: 5: [tvc] Normal termination. Processing time: 1 seconds. 3: Recalibration model: suppressed 3: 3: 3: [tvc] Normal termination. Processing time: 1 seconds. 7/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 1.54 sec 8/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.49 sec 9/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 1.60 sec 4: 4: 4: [tvc] Normal termination. Processing time: 1 seconds. 10/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 1.81 sec 100% tests passed, 0 tests failed out of 10 Total Test time (real) = 1.88 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ cd obj-i686-linux-gnu && make -j22 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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_i386.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.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: 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/119334 and its subdirectories I: Current time: Thu Dec 25 11:03:25 -12 2025 I: pbuilder-time-stamp: 1766703805 Fri Nov 22 16:40:29 UTC 2024 I: 1st build successful. Starting 2nd build on remote node ionos2-i386.debian.net. Fri Nov 22 16:40:29 UTC 2024 I: Preparing to do remote build '2' on ionos2-i386.debian.net. Fri Nov 22 16:40:29 UTC 2024 - checking /var/lib/jenkins/offline_nodes if ionos2-i386.debian.net is marked as down. Fri Nov 22 16:40:29 UTC 2024 - checking via ssh if ionos2-i386.debian.net is up. removed '/tmp/read-only-fs-test-X1T4a2' ==================================================================================== Fri Nov 22 16:40:30 UTC 2024 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos2-i386, called using "2 tvc trixie /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR 5.0.3+git20151221.80e144e+dfsg-5" as arguments. Fri Nov 22 16:40:30 UTC 2024 - actually running "reproducible_build.sh" (md5sum 68e686e434c9ab7bc3ec047d8b309cbc) as "/tmp/jenkins-script-DYpco372" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Fri Nov 22 16:40:30 UTC 2024 I: Downloading source for trixie/tvc=5.0.3+git20151221.80e144e+dfsg-5 Reading package lists... NOTICE: 'tvc' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tvc.git Please use: git clone https://salsa.debian.org/med-team/tvc.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 757 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (dsc) [2227 B] Get:2 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (tar) [745 kB] Get:3 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (diff) [9800 B] Fetched 757 kB in 0s (9429 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'tvc' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/tvc.git Please use: git clone https://salsa.debian.org/med-team/tvc.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 757 kB of source archives. Get:1 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (dsc) [2227 B] Get:2 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (tar) [745 kB] Get:3 http://deb.debian.org/debian trixie/main tvc 5.0.3+git20151221.80e144e+dfsg-5 (diff) [9800 B] Fetched 757 kB in 0s (9429 kB/s) Download complete and in download only mode ============================================================================= Re-Building tvc in trixie on i386 on ionos2-i386 now. Date: Fri Nov 22 17:40:30 CET 2024 Date UTC: Fri Nov 22 16:40:30 UTC 2024 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/pbuilderrc_OQs2 + case ${ARCH} in + let NUM_CPU-=3 + case $ARCH in + locale=de_CH + language=de + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' tvc = debian-installer -o tvc = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' tvc = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo 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.CuoiAxuR/pbuilderrc_OQs2 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Sat Nov 23 06:40:31 +14 2024 I: pbuilder-time-stamp: 1732293631 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-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: using eatmydata during job 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 Tue Sep 6 15:33:36 2022 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/21070/tmp/hooks/D01_modify_environment starting debug: Running on ionos2-i386. 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 Nov 22 16:40 /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/21070/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/21070/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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") BASH_VERSION='5.2.32(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=i386 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' DIRSTACK=() DISTRIBUTION=trixie EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=i686 HOST_ARCH=i386 IFS=' ' INVOCATION_ID=1421180d64e44f22be7ee62d98462ecb LANG=C LANGUAGE=de_CH:de LC_ALL=C LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so MACHTYPE=i686-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=21070 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.CuoiAxuR/pbuilderrc_OQs2 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' SUDO_GID=112 SUDO_UID=107 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://46.16.76.132:3128 I: uname -a Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/21070/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: i386 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 ... 19956 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on libbamtools-dev; however: Package libbamtools-dev is not installed. pbuilder-satisfydepends-dummy depends on libjsoncpp-dev; however: Package libjsoncpp-dev is not installed. pbuilder-satisfydepends-dummy depends on libarmadillo-dev; however: Package libarmadillo-dev is not installed. pbuilder-satisfydepends-dummy depends on libboost-math-dev; however: Package libboost-math-dev is not installed. pbuilder-satisfydepends-dummy depends on libsmithwaterman-dev; however: Package libsmithwaterman-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} comerr-dev{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} krb5-multidev{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libarchive13t64{a} libarmadillo-dev{a} libarmadillo14{a} libarpack2-dev{a} libarpack2t64{a} libbamtools-dev{a} libbamtools2.5.2{a} libblas-dev{a} libblas3{a} libboost-math-dev{a} libboost-math1.83-dev{a} libboost-math1.83.0{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libcom-err2{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdebhelper-perl{a} libdisorder-dev{a} libdisorder0{a} libelf1t64{a} libevent-2.1-7t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libgmp-dev{a} libgmpxx4ldbl{a} libgnutls-dane0t64{a} libgnutls-openssl27t64{a} libgnutls28-dev{a} libgssapi-krb5-2{a} libgssrpc4t64{a} libhdf5-103-1t64{a} libhdf5-cpp-103-1t64{a} libhdf5-dev{a} libhdf5-fortran-102t64{a} libhdf5-hl-100t64{a} libhdf5-hl-cpp-100t64{a} libhdf5-hl-fortran-100t64{a} libicu72{a} libidn2-dev{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjsoncpp-dev{a} libjsoncpp26{a} libk5crypto3{a} libkadm5clnt-mit12{a} libkadm5srv-mit12{a} libkdb5-10t64{a} libkeyutils1{a} libkrb5-3{a} libkrb5-dev{a} libkrb5support0{a} liblapack-dev{a} liblapack3{a} libldap-2.5-0{a} libldap-dev{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libnghttp2-dev{a} libp11-kit-dev{a} libpipeline1{a} libpkgconf3{a} libproc2-0{a} libpsl-dev{a} libpsl5t64{a} librhash1{a} librtmp-dev{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsmithwaterman-dev{a} libsmithwaterman0{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsuperlu-dev{a} libsuperlu6{a} libsuperlu7{a} libsz2{a} libtasn1-6-dev{a} libtool{a} libuchardet0{a} libunbound8{a} libuv1t64{a} libxml2{a} libzstd-dev{a} m4{a} man-db{a} nettle-dev{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules libtasn1-doc linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 76.9 MB of archives. After unpacking 412 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-2 [201 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-5 [1196 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-11 [95.6 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-2 [723 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.30.5-1 [2223 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.1-1+b1 [23.4 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 27 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.18+dfsg-3+b1 [200 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.0-1 [392 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libjsoncpp26 i386 1.9.6-2 [90.0 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 librhash1 i386 1.4.5-1 [144 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 cmake i386 3.30.5-1 [12.5 MB] Get: 42 http://deb.debian.org/debian trixie/main i386 comerr-dev i386 2.1-1.47.1-1+b1 [55.3 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.20 [89.7 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-2 [1631 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 debhelper all 13.20 [915 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 hdf5-helpers i386 1.10.10+repack-4 [23.5 kB] Get: 56 http://deb.debian.org/debian trixie/main i386 libgssrpc4t64 i386 1.21.3-3 [63.1 kB] Get: 57 http://deb.debian.org/debian trixie/main i386 libkadm5clnt-mit12 i386 1.21.3-3 [43.2 kB] Get: 58 http://deb.debian.org/debian trixie/main i386 libkdb5-10t64 i386 1.21.3-3 [45.1 kB] Get: 59 http://deb.debian.org/debian trixie/main i386 libkadm5srv-mit12 i386 1.21.3-3 [57.0 kB] Get: 60 http://deb.debian.org/debian trixie/main i386 krb5-multidev i386 1.21.3-3 [126 kB] Get: 61 http://deb.debian.org/debian trixie/main i386 libaec0 i386 1.1.3-1+b1 [25.0 kB] Get: 62 http://deb.debian.org/debian trixie/main i386 libsz2 i386 1.1.3-1+b1 [8128 B] Get: 63 http://deb.debian.org/debian trixie/main i386 libaec-dev i386 1.1.3-1+b1 [23.0 kB] Get: 64 http://deb.debian.org/debian trixie/main i386 libblas3 i386 3.12.0-3+b1 [143 kB] Get: 65 http://deb.debian.org/debian trixie/main i386 libgfortran5 i386 14.2.0-8 [735 kB] Get: 66 http://deb.debian.org/debian trixie/main i386 liblapack3 i386 3.12.0-3+b1 [2196 kB] Get: 67 http://deb.debian.org/debian trixie/main i386 libarpack2t64 i386 3.9.1-1.1+b1 [101 kB] Get: 68 http://deb.debian.org/debian trixie/main i386 libsuperlu6 i386 6.0.1+dfsg1-1+b1 [172 kB] Get: 69 http://deb.debian.org/debian trixie/main i386 libarmadillo14 i386 1:14.0.1+dfsg-2 [107 kB] Get: 70 http://deb.debian.org/debian trixie/main i386 libblas-dev i386 3.12.0-3+b1 [155 kB] Get: 71 http://deb.debian.org/debian trixie/main i386 liblapack-dev i386 3.12.0-3+b1 [4452 kB] Get: 72 http://deb.debian.org/debian trixie/main i386 libarpack2-dev i386 3.9.1-1.1+b1 [120 kB] Get: 73 http://deb.debian.org/debian trixie/main i386 libhdf5-103-1t64 i386 1.10.10+repack-4 [1186 kB] Get: 74 http://deb.debian.org/debian trixie/main i386 libhdf5-fortran-102t64 i386 1.10.10+repack-4 [98.1 kB] Get: 75 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-100t64 i386 1.10.10+repack-4 [76.0 kB] Get: 76 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-fortran-100t64 i386 1.10.10+repack-4 [41.9 kB] Get: 77 http://deb.debian.org/debian trixie/main i386 libhdf5-cpp-103-1t64 i386 1.10.10+repack-4 [137 kB] Get: 78 http://deb.debian.org/debian trixie/main i386 libhdf5-hl-cpp-100t64 i386 1.10.10+repack-4 [21.9 kB] Get: 79 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Get: 80 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo i386 1:2.1.5-3+b1 [171 kB] Get: 81 http://deb.debian.org/debian trixie/main i386 libjpeg62-turbo-dev i386 1:2.1.5-3+b1 [305 kB] Get: 82 http://deb.debian.org/debian trixie/main i386 libjpeg-dev i386 1:2.1.5-3+b1 [72.2 kB] Get: 83 http://deb.debian.org/debian trixie/main i386 libbrotli-dev i386 1.1.0-2+b6 [313 kB] Get: 84 http://deb.debian.org/debian trixie/main i386 libidn2-dev i386 2.3.7-2+b1 [126 kB] Get: 85 http://deb.debian.org/debian trixie/main i386 libkrb5-dev i386 1.21.3-3 [15.7 kB] Get: 86 http://deb.debian.org/debian trixie/main i386 libldap-dev i386 2.5.18+dfsg-3+b1 [324 kB] Get: 87 http://deb.debian.org/debian trixie/main i386 libpkgconf3 i386 1.8.1-4 [38.4 kB] Get: 88 http://deb.debian.org/debian trixie/main i386 pkgconf-bin i386 1.8.1-4 [30.6 kB] Get: 89 http://deb.debian.org/debian trixie/main i386 pkgconf i386 1.8.1-4 [26.2 kB] Get: 90 http://deb.debian.org/debian trixie/main i386 libnghttp2-dev i386 1.64.0-1 [123 kB] Get: 91 http://deb.debian.org/debian trixie/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB] Get: 92 http://deb.debian.org/debian trixie/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-2+b2 [330 kB] Get: 93 http://deb.debian.org/debian trixie/main i386 libgmp-dev i386 2:6.3.0+dfsg-2+b2 [661 kB] Get: 94 http://deb.debian.org/debian trixie/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB] Get: 95 http://deb.debian.org/debian trixie/main i386 libunbound8 i386 1.22.0-1 [632 kB] Get: 96 http://deb.debian.org/debian trixie/main i386 libgnutls-dane0t64 i386 3.8.8-2 [447 kB] Get: 97 http://deb.debian.org/debian trixie/main i386 libgnutls-openssl27t64 i386 3.8.8-2 [447 kB] Get: 98 http://deb.debian.org/debian trixie/main i386 libp11-kit-dev i386 0.25.5-2+b1 [208 kB] Get: 99 http://deb.debian.org/debian trixie/main i386 libtasn1-6-dev i386 4.19.0-3+b3 [102 kB] Get: 100 http://deb.debian.org/debian trixie/main i386 nettle-dev i386 3.10-1+b1 [1334 kB] Get: 101 http://deb.debian.org/debian trixie/main i386 libgnutls28-dev i386 3.8.8-2 [1453 kB] Get: 102 http://deb.debian.org/debian trixie/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-2+b5 [72.3 kB] Get: 103 http://deb.debian.org/debian trixie/main i386 libssl-dev i386 3.3.2-2 [2790 kB] Get: 104 http://deb.debian.org/debian trixie/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB] Get: 105 http://deb.debian.org/debian trixie/main i386 libzstd-dev i386 1.5.6+dfsg-1+b1 [355 kB] Get: 106 http://deb.debian.org/debian trixie/main i386 libcurl4-openssl-dev i386 8.11.0-1 [520 kB] Get: 107 http://deb.debian.org/debian trixie/main i386 libhdf5-dev i386 1.10.10+repack-4 [2783 kB] Get: 108 http://deb.debian.org/debian trixie/main i386 libsuperlu7 i386 7.0.0+dfsg1-2 [175 kB] Get: 109 http://deb.debian.org/debian trixie/main i386 libsuperlu-dev i386 7.0.0+dfsg1-2 [21.9 kB] Get: 110 http://deb.debian.org/debian trixie/main i386 libarmadillo-dev i386 1:14.0.1+dfsg-2 [413 kB] Get: 111 http://deb.debian.org/debian trixie/main i386 libbamtools2.5.2 i386 2.5.2+dfsg-6+b1 [178 kB] Get: 112 http://deb.debian.org/debian trixie/main i386 libbamtools-dev i386 2.5.2+dfsg-6+b1 [242 kB] Get: 113 http://deb.debian.org/debian trixie/main i386 libboost1.83-dev i386 1.83.0-3.2+b1 [10.6 MB] Get: 114 http://deb.debian.org/debian trixie/main i386 libboost-math1.83.0 i386 1.83.0-3.2+b1 [433 kB] Get: 115 http://deb.debian.org/debian trixie/main i386 libboost-math1.83-dev i386 1.83.0-3.2+b1 [511 kB] Get: 116 http://deb.debian.org/debian trixie/main i386 libboost-math-dev i386 1.83.0.2+b2 [3800 B] Get: 117 http://deb.debian.org/debian trixie/main i386 libdisorder0 i386 0.0.2+git20130809.8062ee1-4+b2 [4860 B] Get: 118 http://deb.debian.org/debian trixie/main i386 libdisorder-dev i386 0.0.2+git20130809.8062ee1-4+b2 [4868 B] Get: 119 http://deb.debian.org/debian trixie/main i386 libjsoncpp-dev i386 1.9.6-2 [24.9 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libsmithwaterman0 i386 0.0+git20160702.2610e25-12+b2 [38.7 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libsmithwaterman-dev i386 0.0+git20160702.2610e25-12+b2 [43.4 kB] Fetched 76.9 MB in 1s (65.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (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 ... 19956 files and directories currently installed.) Preparing to unpack .../000-libproc2-0_2%3a4.0.4-6_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../001-procps_2%3a4.0.4-6_i386.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../002-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../003-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../004-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../005-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../006-gettext-base_0.22.5-2_i386.deb ... Unpacking gettext-base (0.22.5-2) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../007-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../008-groff-base_1.23.0-5_i386.deb ... Unpacking groff-base (1.23.0-5) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../009-bsdextrautils_2.40.2-11_i386.deb ... Unpacking bsdextrautils (2.40.2-11) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../010-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../011-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../012-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../013-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../014-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../015-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../016-autopoint_0.22.5-2_all.deb ... Unpacking autopoint (0.22.5-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../017-cmake-data_3.30.5-1_all.deb ... Unpacking cmake-data (3.30.5-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../018-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../019-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:i386. Preparing to unpack .../020-libarchive13t64_3.7.4-1.1_i386.deb ... Unpacking libarchive13t64:i386 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../021-libbrotli1_1.1.0-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b6) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../022-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../023-libcom-err2_1.47.1-1+b1_i386.deb ... Unpacking libcom-err2:i386 (1.47.1-1+b1) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../024-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../025-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../026-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../027-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../028-libsasl2-modules-db_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../029-libsasl2-2_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../030-libldap-2.5-0_2.5.18+dfsg-3+b1_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.18+dfsg-3+b1) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../031-libnghttp2-14_1.64.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:i386. Preparing to unpack .../032-libpsl5t64_0.21.2-1.1+b1_i386.deb ... Unpacking libpsl5t64:i386 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../033-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:i386. Preparing to unpack .../034-libssh2-1t64_1.11.1-1_i386.deb ... Unpacking libssh2-1t64:i386 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:i386. Preparing to unpack .../035-libcurl4t64_8.11.0-1_i386.deb ... Unpacking libcurl4t64:i386 (8.11.0-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../036-libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package libjsoncpp26:i386. Preparing to unpack .../037-libjsoncpp26_1.9.6-2_i386.deb ... Unpacking libjsoncpp26:i386 (1.9.6-2) ... Selecting previously unselected package librhash1:i386. Preparing to unpack .../038-librhash1_1.4.5-1_i386.deb ... Unpacking librhash1:i386 (1.4.5-1) ... Selecting previously unselected package libuv1t64:i386. Preparing to unpack .../039-libuv1t64_1.48.0-7_i386.deb ... Unpacking libuv1t64:i386 (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../040-cmake_3.30.5-1_i386.deb ... Unpacking cmake (3.30.5-1) ... Selecting previously unselected package comerr-dev:i386. Preparing to unpack .../041-comerr-dev_2.1-1.47.1-1+b1_i386.deb ... Unpacking comerr-dev:i386 (2.1-1.47.1-1+b1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../042-libdebhelper-perl_13.20_all.deb ... Unpacking libdebhelper-perl (13.20) ... Selecting previously unselected package libtool. Preparing to unpack .../043-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../044-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../045-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../046-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../047-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../048-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../049-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../050-gettext_0.22.5-2_i386.deb ... Unpacking gettext (0.22.5-2) ... Selecting previously unselected package intltool-debian. 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Setting up libaec0:i386 (1.1.3-1+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libpsl-dev:i386 (0.21.2-1.1+b1) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up libblas3:i386 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libunbound8:i386 (1.22.0-1) ... Setting up libpkgconf3:i386 (1.8.1-4) ... Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-2+b2) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-3+b1) ... Setting up libgnutls-dane0t64:i386 (3.8.8-2) ... Setting up libjpeg62-turbo-dev:i386 (1:2.1.5-3+b1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:i386 (1.9.6-2) ... Setting up libproc2-0:i386 (2:4.0.4-6) ... Setting up comerr-dev:i386 (2.1-1.47.1-1+b1) ... Setting up libssl-dev:i386 (3.3.2-2) ... Setting up autopoint (0.22.5-2) ... Setting up pkgconf-bin (1.8.1-4) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libdisorder-dev:i386 (0.0.2+git20130809.8062ee1-4+b2) ... Setting up libbamtools2.5.2:i386 (2.5.2+dfsg-6+b1) ... Setting up libidn2-dev:i386 (2.3.7-2+b1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ... Setting up libgfortran5:i386 (14.2.0-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up cmake-data (3.30.5-1) ... Setting up librhash1:i386 (1.4.5-1) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libssh2-1t64:i386 (1.11.1-1) ... Setting up libboost-math1.83.0:i386 (1.83.0-3.2+b1) ... Setting up libtasn1-6-dev:i386 (4.19.0-3+b3) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libbrotli-dev:i386 (1.1.0-2+b6) ... Setting up libp11-kit-dev:i386 (0.25.5-2+b1) ... Setting up libblas-dev:i386 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode Setting up libsz2:i386 (1.1.3-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libjsoncpp-dev:i386 (1.9.6-2) ... Setting up liblapack3:i386 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up gettext (0.22.5-2) ... Setting up libarpack2t64:i386 (3.9.1-1.1+b1) ... Setting up libgmp-dev:i386 (2:6.3.0+dfsg-2+b2) ... Setting up nettle-dev:i386 (3.10-1+b1) ... 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Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-5) ... Setting up libarmadillo14 (1:14.0.1+dfsg-2) ... Setting up libsuperlu-dev:i386 (7.0.0+dfsg1-2) ... Setting up libarchive13t64:i386 (3.7.4-1.1) ... Setting up libgnutls28-dev:i386 (3.8.8-2) ... Setting up libnghttp2-dev:i386 (1.64.0-1) ... Setting up libarpack2-dev:i386 (3.9.1-1.1+b1) ... Setting up libcurl4t64:i386 (8.11.0-1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgssrpc4t64:i386 (1.21.3-3) ... Setting up librtmp-dev:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up cmake (3.30.5-1) ... Setting up libhdf5-103-1t64:i386 (1.10.10+repack-4) ... Setting up libkadm5clnt-mit12:i386 (1.21.3-3) ... Setting up libhdf5-hl-100t64:i386 (1.10.10+repack-4) ... Setting up libkdb5-10t64:i386 (1.21.3-3) ... Setting up libhdf5-cpp-103-1t64:i386 (1.10.10+repack-4) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: user script /srv/workspace/pbuilder/21070/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for trixie I: user script /srv/workspace/pbuilder/21070/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Mohammed Bilal dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config 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/i386-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:2 (cmake_minimum_required): Compatibility with CMake < 3.5 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 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- 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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' -- Configuring done (0.7s) -- Generating done (0.0s) 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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu dh_auto_build cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/tvcutils/unify_vcf.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp [ 20%] Building CXX object CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvcutils.dir/VariantCaller/TargetsManager.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp [ 21%] Building CXX object CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -MF CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o.d -o CMakeFiles/tvcutils.dir/Util/OptArgs.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util/OptArgs.cpp [ 23%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/Variant.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/Variant.cpp [ 24%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/split.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/split.cpp [ 26%] Building CXX object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -MF CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o.d -o CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/tabix.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/tabix.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] 36 | arma::set_stream_err1(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/armadillo:411, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: /usr/include/armadillo_bits/debug.hpp:83:1: note: declared here 83 | set_stream_err1(const std::ostream&) | ^~~~~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:37:24: warning: 'void arma::set_stream_err2(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] 37 | arma::set_stream_err2(null_ostream); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/armadillo_bits/debug.hpp:92:1: note: declared here 92 | set_stream_err2(const std::ostream&) | ^~~~~~~~~~~~~~~ [ 27%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/index.c [ 29%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/bgzf.c.o /usr/bin/cc -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c In file included from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.h:64, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:19: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp: In instantiation of 'void markov_chain::optimal_path() [with T = unsigned int]': /build/reproducible-path/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 = unsigned int]' 64 | optimal_path(); | ^~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:38:13: required from 'markov_chain::markov_chain(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; T = unsigned int]' 38 | initialize(begin, end, *(m.first), *(m.second)); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:550:69: required from here 550 | markov_chain ch(depth_values.begin(), depth_values.end()); | ^ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/viterbi.hpp:114:13: warning: ignoring return value of 'constexpr bool std::operator!=(const reverse_iterator<_Iterator>&, const reverse_iterator<_Iterator>&) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >]', declared with attribute 'nodiscard' [-Wunused-result] 114 | for (; it != rend(), vit != values.rend(); it++, vit++) { | ~~~^~~~~~~~~ In file included from /usr/include/c++/14/string:48, from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/tvcutils/unify_vcf.cpp:7: /usr/include/c++/14/bits/stl_iterator.h:455:5: note: declared here 455 | operator!=(const reverse_iterator<_Iterator>& __x, | ^~~~~~~~ /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c: In function '_bgzf_check_EOF': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib/tabixpp/bgzf.c:678:9: warning: ignoring return value of 'fread' declared with attribute 'warn_unused_result' [-Wunused-result] 678 | fread(buf, 1, 28, fp->file); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object CMakeFiles/tvcutils.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvcutils.dir/IonVersion.cpp.o -MF CMakeFiles/tvcutils.dir/IonVersion.cpp.o.d -o CMakeFiles/tvcutils.dir/IonVersion.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/IonVersion.cpp [ 32%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/OrderedBAMWriter.cpp [ 33%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/SampleManager.cpp [ 35%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/TargetsManager.cpp [ 36%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HandleVariant.cpp [ 38%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HotspotReader.cpp [ 40%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/MetricsManager.cpp [ 41%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval 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-ffile-prefix-map=/build/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice/SpliceVariantHypotheses.cpp [ 56%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller 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-ffile-prefix-map=/build/reproducible-path/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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/DecisionTreeData.cpp [ 58%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval 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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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HypothesisEvaluator.cpp [ 61%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -MF CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/DiagnosticJSON.cpp /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp: In function 'double VariantAssist::MannWhitneyU(std::vector&, std::vector&, bool)': /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:191:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 'unsigned int'} [-Wformat=] 191 | fprintf(stdout, "ref.size()=%lu; ", ref.size()); | ~~^ ~~~~~~~~~~ | | | | | std::vector::size_type {aka unsigned int} | long unsigned int | %u /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter/VariantAssist.cpp:192:36: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'std::vector::size_type' {aka 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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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [ 63%] Built target tvcutils [ 64%] Building CXX object CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE 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-I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MT CMakeFiles/tvc.dir/file-io/ion_error.c.o -MF CMakeFiles/tvc.dir/file-io/ion_error.c.o.d -o CMakeFiles/tvc.dir/file-io/ion_error.c.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io/ion_error.c [ 96%] Building CXX object CMakeFiles/tvc.dir/IonVersion.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/IonVersion.cpp [ 98%] Building CXX object CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o /usr/bin/c++ -DALIGNSTATS_IGNORE -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/vcflib -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/external/freebayes/src -I/usr/include/jsoncpp -I/usr/include/bamtools -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/FlowDistEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Bookkeeping -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Reads -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Splice -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/Filter -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/realignment -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/file-io -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Calibration -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/Util -I/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3 -MD -MT CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -MF CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o.d -o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/BaseCaller/TreephaserSSE.cpp [100%] Linking CXX executable tvc /usr/bin/cmake -E cmake_link_script CMakeFiles/tvc.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/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/tvc.dir/VariantCaller/VariantCaller.cpp.o CMakeFiles/tvc.dir/VariantCaller/BAMWalkerEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/OrderedBAMWriter.cpp.o CMakeFiles/tvc.dir/VariantCaller/SampleManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/TargetsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/HandleVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o CMakeFiles/tvc.dir/VariantCaller/MetricsManager.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/MiscUtil.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/ExtendParameters.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/InputStructures.cpp.o CMakeFiles/tvc.dir/VariantCaller/Bookkeeping/VcfFormat.cpp.o CMakeFiles/tvc.dir/VariantCaller/Reads/ExtendedReadInfo.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ErrorMotifs.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/LocalContext.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/ClassifyVariant.cpp.o CMakeFiles/tvc.dir/VariantCaller/Splice/SpliceVariantHypotheses.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/DecisionTreeData.cpp.o CMakeFiles/tvc.dir/VariantCaller/Filter/VariantAssist.cpp.o CMakeFiles/tvc.dir/VariantCaller/HypothesisEvaluator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/DiagnosticJSON.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/BiasGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SigmaGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/SkewGenerator.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/PosteriorInference.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/ShortStack.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/StackEngine.cpp.o CMakeFiles/tvc.dir/VariantCaller/EnsembleEval/CrossHypotheses.cpp.o CMakeFiles/tvc.dir/external/vcflib/Variant.cpp.o CMakeFiles/tvc.dir/external/vcflib/split.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/tabix.cpp.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/index.c.o CMakeFiles/tvc.dir/external/vcflib/tabixpp/bgzf.c.o CMakeFiles/tvc.dir/external/freebayes/src/AlleleParser.cpp.o CMakeFiles/tvc.dir/BaseCaller/PIDloop.cpp.o CMakeFiles/tvc.dir/BaseCaller/DPTreephaser.cpp.o CMakeFiles/tvc.dir/Calibration/LinearCalibrationModel.cpp.o CMakeFiles/tvc.dir/Calibration/FlowAlignment.cpp.o CMakeFiles/tvc.dir/Util/OptArgs.cpp.o CMakeFiles/tvc.dir/realignment/Realigner.cpp.o "CMakeFiles/tvc.dir/file-io/ion_util.c.o" "CMakeFiles/tvc.dir/file-io/ion_error.c.o" CMakeFiles/tvc.dir/IonVersion.cpp.o CMakeFiles/tvc.dir/BaseCaller/TreephaserSSE.cpp.o -o tvc -lbamtools -lz -lpthread -lblas -llapack -larmadillo -ljsoncpp -lsmithwaterman -ldisorder make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' [100%] Built target tvc make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' dh_auto_test cd obj-i686-linux-gnu && make -j10 test ARGS\+=--verbose ARGS\+=-j10 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j10 UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc 1: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 1: Test timeout computed to be: 10000000 test 2 Start 2: tvc_test_1_thread_sse_on 2: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 2: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 2: Test timeout computed to be: 10000000 test 3 Start 3: tvc_test_1_thread_sse_off 3: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "1" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test1" "--output-vcf" "small_variants.vcf" 3: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "on" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 4: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvc "--input-bam" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test.bam" "--reference" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/reference.fasta" "--target-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed" "--error-motifs" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/sse/motifset.txt" "--parameters-file" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json" "--use-sse-basecaller" "off" "--trim-ampliseq-primers" "on" "--num-threads" "4" "--output-dir" "/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/test2" "--output-vcf" "small_variants.vcf" 5: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 5: Test timeout computed to be: 10000000 test 6 Start 6: tvcutils_call 6: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils 6: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 6: Test timeout computed to be: 10000000 test 7 Start 7: tvcutils_prepare_hotspots_call 7: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "prepare_hotspots" 7: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 7: Test timeout computed to be: 10000000 test 8 Start 8: tvcutils_validate_bed_call 8: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "validate_bed" 8: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 8: Test timeout computed to be: 10000000 test 9 Start 9: tvcutils_unify_vcf_call 9: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcutils "unify_vcf" 9: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 9: Test timeout computed to be: 10000000 test 10 Start 10: tvcassembly_call 10: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcassembly 10: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 10: Test timeout computed to be: 10000000 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: 1/10 Test #6: tvcutils_call .................................... Passed 0.01 sec 2/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec 3/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.01 sec 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: 4/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.01 sec 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: 5/10 Test #10: tvcassembly_call ................................. Passed 0.01 sec 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: 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) 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) 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! 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! 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! 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/reproducible-path/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 3: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 3: TargetsManager: 1 target(s) 3: TargetsManager: Trimming of AmpliSeq primers is enabled 2: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed 2: TargetsManager: 1 target(s) 2: TargetsManager: Trimming of AmpliSeq primers is enabled 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/reproducible-path/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 6/10 Test #1: tvc_call ......................................... Passed 0.03 sec 4: SampleManager: Found 1 read group(s) and 1 sample(s). 4: SampleManager: Primary sample "85" (default) present in 1 read group(s) 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 4: TVC found a total of 1 different flow orders of max flow lengths: 500 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 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 4: Recalibration was detected from comment lines in bam file(s): 4: 1 unique blocks of recalibration info detected. 4: Loading systematic error contexts. 3: Recalibration was detected from comment lines in bam file(s): 3: 1 unique blocks of recalibration info detected. 3: Loading systematic error contexts. 5: Recalibration was detected from comment lines in bam file(s): 5: 1 unique blocks of recalibration info detected. 5: Loading systematic error contexts. 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: Loaded. 4: Loaded. 2: Loaded. 5: Loaded. 4: 4: 4: [tvc] Normal termination. Processing time: 1 seconds. 3: Recalibration model: suppressed 3: 3: 3: [tvc] Normal termination. Processing time: 1 seconds. 2: Recalibration model: suppressed 2: 2: 2: [tvc] Normal termination. Processing time: 1 seconds. 5: 5: 5: [tvc] Normal termination. Processing time: 1 seconds. 7/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 1.19 sec 8/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 1.19 sec 9/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 1.21 sec 10/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.26 sec 100% tests passed, 0 tests failed out of 10 Total Test time (real) = 1.27 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvc -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcassembly -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/tvcutils -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-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/tvc debian/tvc/usr/bin/tvcutils were not linked against libdisorder.so.0 (they use none of the library's symbols) dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb'. dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_i386.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.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/21070/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/21070/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/21070 and its subdirectories I: Current time: Sat Nov 23 06:42:20 +14 2024 I: pbuilder-time-stamp: 1732293740 + false + set +x Fri Nov 22 16:42:20 UTC 2024 I: Signing ./b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo as tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc Fri Nov 22 16:42:20 UTC 2024 I: Signed ./b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo as ./b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc Fri Nov 22 16:42:20 UTC 2024 - build #2 for tvc/trixie/i386 on ionos2-i386 done. Starting cleanup. All cleanup done. Fri Nov 22 16:42:20 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-DYpco372, removing. /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR: total 276 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 16:40 b1 drwxr-xr-x 2 jenkins jenkins 4096 Nov 22 16:42 b2 -rw------- 1 jenkins jenkins 264582 Nov 22 16:40 rbuildlog.Kw0KWkO -rw-r--r-- 1 jenkins jenkins 2227 Sep 6 2022 tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b1: total 12812 -rw-r--r-- 1 jenkins jenkins 260879 Nov 22 16:40 build.log -rw-r--r-- 1 jenkins jenkins 11624408 Nov 22 16:40 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_i386.deb -rw-r--r-- 1 jenkins jenkins 9800 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2227 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc -rw-r--r-- 1 jenkins jenkins 8420 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 9302 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1747 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes -rw-r--r-- 1 jenkins jenkins 1158148 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb -rw-r--r-- 1 jenkins jenkins 1599 Nov 22 16:40 tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b2: total 12792 -rw-r--r-- 1 jenkins jenkins 262781 Nov 22 16:42 build.log -rw-r--r-- 1 jenkins jenkins 11624408 Nov 22 16:42 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_i386.deb -rw-r--r-- 1 jenkins jenkins 9800 Nov 22 16:42 tvc_5.0.3+git20151221.80e144e+dfsg-5.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2227 Nov 22 16:42 tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc -rw-r--r-- 1 jenkins jenkins 8420 Nov 22 16:42 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo -rw-r--r-- 1 jenkins jenkins 9302 Nov 22 16:42 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1747 Nov 22 16:42 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes -rw-r--r-- 1 jenkins jenkins 1158148 Nov 22 16:42 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb -rw-r--r-- 1 jenkins jenkins 1599 Nov 22 16:42 tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes Fri Nov 22 16:42:21 UTC 2024 I: Deleting $TMPDIR on ionos2-i386.debian.net. Fri Nov 22 16:42:21 UTC 2024 I: tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes: Format: 1.8 Date: Mon, 05 Sep 2022 17:20:03 +0000 Source: tvc Binary: tvc tvc-dbgsym Architecture: i386 Version: 5.0.3+git20151221.80e144e+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Mohammed Bilal Description: tvc - genetic variant caller for Ion Torrent sequencing platforms Changes: tvc (5.0.3+git20151221.80e144e+dfsg-5) unstable; urgency=medium . * Team upload. * Add autopkgtest * Standards-Version: 4.6.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. Checksums-Sha1: 76e1447aa9950809af47716632c5ad67da34e404 11624408 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_i386.deb db829895b206cdbcce5c34ddb7000ac9599b437a 8420 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo 1f4a14c18a5f1d16c168ef66a7da747a9a8b5d95 1158148 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb Checksums-Sha256: 6d1e07dc6d93c993cc3e47e0c918c8b3e7e0f05b5405fd3ee199494c37f9f4e2 11624408 tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_i386.deb 4aa2007e5c2b21fcbf057cd2d19e3cd4b8f7d4d94f6070c665b25b1fe835371f 8420 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo 5c05a394361c84137d4bbbf0fde6703cc3d1da31ab7e56d5385b43cec6b8be9e 1158148 tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb Files: c261baa4d8a7a6c58dc6c371346b433e 11624408 debug optional tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_i386.deb 0ecb56a853bc4b9dcab74c1d0feb55c4 8420 science optional tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo 7237a8e44fad975357044af02d689778 1158148 science optional tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2024-11-22 16:40:27.830851292 +0000 +++ b2/build.log 2024-11-22 16:42:21.189719425 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Dec 25 11:01:12 -12 2025 -I: pbuilder-time-stamp: 1766703672 +I: Current time: Sat Nov 23 06:40:31 +14 2024 +I: pbuilder-time-stamp: 1732293631 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -36,54 +36,86 @@ dpkg-source: info: applying gcc11.patch I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/119334/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/21070/tmp/hooks/D01_modify_environment starting +debug: Running on ionos2-i386. +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 Nov 22 16:40 /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/21070/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/21070/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='i386' + 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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=10 ' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='a3f0ea36e7ed41d2bcec0502d6e4e926' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='119334' - PS1='# ' - PS2='> ' + INVOCATION_ID=1421180d64e44f22be7ee62d98462ecb + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-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=21070 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/pbuilderrc_E8YS --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b1 --logfile b1/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://213.165.73.152:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/pbuilderrc_OQs2 --distribution trixie --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b2 --logfile b2/build.log tvc_5.0.3+git20151221.80e144e+dfsg-5.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://46.16.76.132:3128 I: uname -a - Linux ionos6-i386 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-27-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.115-1 (2024-11-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/119334/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/21070/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -252,7 +284,7 @@ Get: 119 http://deb.debian.org/debian trixie/main i386 libjsoncpp-dev i386 1.9.6-2 [24.9 kB] Get: 120 http://deb.debian.org/debian trixie/main i386 libsmithwaterman0 i386 0.0+git20160702.2610e25-12+b2 [38.7 kB] Get: 121 http://deb.debian.org/debian trixie/main i386 libsmithwaterman-dev i386 0.0+git20160702.2610e25-12+b2 [43.4 kB] -Fetched 76.9 MB in 1s (73.0 MB/s) +Fetched 76.9 MB in 1s (65.4 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:i386. (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 ... 19956 files and directories currently installed.) @@ -756,7 +788,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes +I: user script /srv/workspace/pbuilder/21070/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/21070/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../tvc_5.0.3+git20151221.80e144e+dfsg-5_source.changes dpkg-buildpackage: info: source package tvc dpkg-buildpackage: info: source version 5.0.3+git20151221.80e144e+dfsg-5 dpkg-buildpackage: info: source distribution unstable @@ -793,7 +829,7 @@ -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_CXX_FLAGS: '-g -O2 -ffile-prefix-map=/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -msse3' --- Configuring done (1.3s) +-- Configuring done (0.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -810,7 +846,7 @@ -- Build files have been written to: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu dh_auto_build - cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j10 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -822,100 +858,71 @@ make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcassembly.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles/tvcutils.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' cd /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg 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'/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvcassembly.dir/build.make CMakeFiles/tvcassembly.dir/build -make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make -f CMakeFiles/tvc.dir/build.make CMakeFiles/tvc.dir/build +make -f CMakeFiles/tvcutils.dir/build.make CMakeFiles/tvcutils.dir/build make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -[ 1%] Building CXX object 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-MF CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o.d -o CMakeFiles/tvc.dir/VariantCaller/HotspotReader.cpp.o -c /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/HotspotReader.cpp -[ 35%] Building C object CMakeFiles/tvcutils.dir/external/vcflib/tabixpp/index.c.o +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': +/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] + 36 | arma::set_stream_err1(null_ostream); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +In file included from /usr/include/armadillo:411, + from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: 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/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/EnsembleEval/CrossHypotheses.cpp -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp: In function 'void TheSilenceOfTheArmadillos(std::ofstream&)': -/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:36:24: warning: 'void arma::set_stream_err1(const std::ostream&)' is deprecated: this function does nothing; instead use ARMA_CERR_STREAM or ARMA_WARN_LEVEL; see documentation [-Wdeprecated-declarations] - 36 | arma::set_stream_err1(null_ostream); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -In file included from /usr/include/armadillo:411, - from /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/VariantCaller/VariantCaller.cpp:12: -/usr/include/armadillo_bits/debug.hpp:83:1: note: declared here - 83 | set_stream_err1(const std::ostream&) - | ^~~~~~~~~~~~~~~ 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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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' -[100%] Built target tvcutils +[100%] Built target tvc make[2]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' dh_auto_test - cd obj-i686-linux-gnu && make -j22 test ARGS\+=--verbose ARGS\+=-j22 + cd obj-i686-linux-gnu && make -j10 test ARGS\+=--verbose ARGS\+=-j10 make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j22 +/usr/bin/ctest --force-new-ctest-process --verbose -j10 UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu @@ -1115,6 +1151,99 @@ 10: Test command: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu/tvcassembly 10: Working Directory: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu 10: Test timeout computed to be: 10000000 +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: + 1/10 Test #6: tvcutils_call .................................... Passed 0.01 sec + 2/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.01 sec + 3/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.01 sec +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: + 4/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.01 sec +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: + 5/10 Test #10: tvcassembly_call ................................. Passed 0.01 sec 1: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 1: 1: Usage: tvc [options] @@ -1239,6 +1368,74 @@ 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: +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) 2: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 2: 2: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf @@ -1310,160 +1507,6 @@ 2: process-input-positions-only = false (boolean, builtin default) 2: suppress-recalibration = true (boolean, builtin default) 2: resolve-clipped-bases = false (boolean, builtin default) -2: prefix-exclude = 6 -2: allow-indels = true (boolean, builtin default) -2: allow-snps = true (boolean, builtin default) -2: allow-mnps = true (boolean, builtin default) -2: allow-complex = false (boolean, builtin default) -2: left-align-indels = false (boolean, builtin default) -2: use-best-n-alleles = 2 (integer, builtin default) -2: use-input-allele-only = false (boolean, builtin default) -2: min-mapping-qv = 4 (integer, builtin default) -2: read-snp-limit = 10 (integer, builtin default) -2: read-max-mismatch-fraction = 1 (double, builtin default) -2: max-complex-gap = 1 (integer, builtin default) -2: gen-min-alt-allele-freq = 0.2 (double, builtin default) -2: gen-min-coverage = 6 (integer, builtin default) -2: gen-min-indel-alt-allele-freq = 0.2 (double, builtin default) -2: override-limits = false (boolean, builtin default) -2: Limit check parameter hp-max-length: lim. 1 <= 8? OK! -2: Limit check parameter sse-prob-threshold: lim. 0 <= 0.2 <= lim. 1? OK! -2: Limit check parameter min-ratio-reads-non-sse-strand: lim. 0 <= 0.2 <= lim. 1? OK! -2: Limit check parameter sse-relative-safety-level: lim. 0 <= 0.025 <= lim. 1? OK! -2: Limit check parameter realignment-threshold: lim. 0 <= 1 <= lim. 1? OK! -2: Limit check parameter data-quality-stringency: lim. 0 <= 4? OK! -2: Limit check parameter read-rejection-threshold: lim. 0 <= 0.5 <= lim. 1? OK! -2: Limit check parameter downsample-to-coverage: lim. 20 <= 2000 <= lim. 100000? OK! -2: Limit check parameter position-bias-ref-fraction: lim. 0 <= 0.05 <= lim. 1? OK! -2: Limit check parameter position-bias: lim. 0 <= 0.75 <= lim. 1? OK! -2: Limit check parameter position-bias-pval: lim. 0 <= 0.05 <= lim. 1? OK! -2: Limit check parameter tune-sbias: lim. 0.001 <= 0.01 <= lim. 1000? OK! -2: Limit check parameter snp-min-cov-each-strand: lim. 0 <= 0? OK! -2: Limit check parameter snp-min-variant-score: lim. 0 <= 10? OK! -2: Limit check parameter snp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -2: Limit check parameter snp-min-coverage: lim. 0 <= 6? OK! -2: Limit check parameter snp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! -2: Limit check parameter snp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! -2: Limit check parameter mnp-min-cov-each-strand: lim. 0 <= 0? OK! -2: Limit check parameter mnp-min-variant-score: lim. 0 <= 10? OK! -2: Limit check parameter mnp-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -2: Limit check parameter mnp-min-coverage: lim. 0 <= 6? OK! -2: Limit check parameter mnp-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! -2: Limit check parameter mnp-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! -2: Limit check parameter indel-min-cov-each-strand: lim. 0 <= 1? OK! -2: Limit check parameter indel-min-variant-score: lim. 0 <= 10? OK! -2: Limit check parameter indel-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -2: Limit check parameter indel-min-coverage: lim. 0 <= 15? OK! -2: Limit check parameter indel-strand-bias: lim. 0.5 <= 0.85 <= lim. 1? OK! -2: Limit check parameter indel-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! -2: Limit check parameter hotspot-min-cov-each-strand: lim. 0 <= 0? OK! -2: Limit check parameter hotspot-min-variant-score: lim. 0 <= 10? OK! -2: Limit check parameter hotspot-min-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -2: Limit check parameter hotspot-min-coverage: lim. 0 <= 6? OK! -2: Limit check parameter hotspot-strand-bias: lim. 0.5 <= 0.95 <= lim. 1? OK! -2: Limit check parameter hotspot-strand-bias-pval: lim. 0 <= 1 <= lim. 1? OK! -2: Limit check parameter max-flows-to-test: lim. 1 <= 10 <= lim. 100? OK! -2: Limit check parameter min-delta-for-flow: lim. 0.01 <= 0.1 <= lim. 0.5? OK! -2: Limit check parameter prediction-precision: lim. 0.1 <= 30? OK! -2: Limit check parameter outlier-probability: lim. 0 <= 0.01 <= lim. 1? OK! -2: Limit check parameter germline-prior-strength: lim. 0 <= 0 <= lim. 1000? OK! -2: Limit check parameter heavy-tailed: lim. 1 <= 3? OK! -2: Limit check parameter filter-unusual-predictions: lim. 0 <= 0.3? OK! -2: Limit check parameter soft-clip-bias-checker: lim. 0 <= 0.1 <= lim. 1? OK! -2: Limit check parameter filter-deletion-predictions: lim. 0 <= 100? OK! -2: Limit check parameter filter-insertion-predictions: lim. 0 <= 100? OK! -2: Limit check parameter max-detail-level: lim. 0 <= 0 <= lim. 10000? OK! -2: Limit check parameter shift-likelihood-penalty: lim. 0.01 <= 0.3? OK! -2: Limit check parameter minimum-sigma-prior: lim. 0.01 <= 0.085? OK! -2: Limit check parameter slope-sigma-prior: lim. 0 <= 0.0084? OK! -2: Limit check parameter sigma-prior-weight: lim. 0.01 <= 1? OK! -2: Limit check parameter k-zero: lim. 0 <= 3? OK! -2: Limit check parameter num-threads: lim. 1 <= 1 <= lim. 128? OK! -2: Limit check parameter num-variants-per-thread: lim. 1 <= 250 <= lim. 10000? OK! -2: Limit check parameter use-best-n-alleles: lim. 0 <= 2 <= lim. 20? OK! -2: Limit check parameter min-mapping-qv: lim. 0 <= 4? OK! -2: Limit check parameter read-snp-limit: lim. 0 <= 10? OK! -2: Limit check parameter read-max-mismatch-fraction: lim. 0 <= 1 <= lim. 1? OK! -2: Limit check parameter gen-min-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -2: Limit check parameter gen-min-coverage: lim. 0 <= 6? OK! -2: Limit check parameter gen-min-indel-alt-allele-freq: lim. 0 <= 0.2 <= lim. 1? OK! -2: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed -2: TargetsManager: 1 target(s) -2: TargetsManager: Trimming of AmpliSeq primers is enabled -2: SampleManager: Found 1 read group(s) and 1 sample(s). -2: SampleManager: Primary sample "85" (default) present in 1 read group(s) -2: TVC found a total of 1 different flow orders of max flow lengths: 500 -2: Recalibration was detected from comment lines in bam file(s): -2: 1 unique blocks of recalibration info detected. -2: Loading systematic error contexts. -3: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller -3: -3: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf -3: hp-max-length = 8 (integer, 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) @@ -1544,15 +1587,83 @@ 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/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed -3: TargetsManager: 1 target(s) -3: TargetsManager: Trimming of AmpliSeq primers is enabled -3: SampleManager: Found 1 read group(s) and 1 sample(s). -3: SampleManager: Primary sample "85" (default) present in 1 read group(s) -3: TVC found a total of 1 different flow orders of max flow lengths: 500 -3: Recalibration was detected from comment lines in bam file(s): -3: 1 unique blocks of recalibration info detected. -3: Loading systematic error contexts. +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! 4: tvc 5.0-3 (e975447-9fa85fb) - Torrent Variant Caller 4: 4: INFO: No input VCF (Hotspot) file specified via -c,--input-vcf @@ -1668,48 +1779,6 @@ 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/reproducible-path/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 @@ -1861,110 +1930,84 @@ 5: TargetsManager: Loaded targets file /build/reproducible-path/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 +3: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed +3: TargetsManager: 1 target(s) +3: TargetsManager: Trimming of AmpliSeq primers is enabled +2: TargetsManager: Loaded targets file /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/share/TVC/examples/example1/test_unmerged_detail.bed +2: TargetsManager: 1 target(s) +2: TargetsManager: Trimming of AmpliSeq primers is enabled +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/reproducible-path/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 + 6/10 Test #1: tvc_call ......................................... Passed 0.03 sec +4: SampleManager: Found 1 read group(s) and 1 sample(s). +4: SampleManager: Primary sample "85" (default) present in 1 read group(s) 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 +4: TVC found a total of 1 different flow orders of max flow lengths: 500 +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 +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 +4: Recalibration was detected from comment lines in bam file(s): +4: 1 unique blocks of recalibration info detected. +4: Loading systematic error contexts. +3: Recalibration was detected from comment lines in bam file(s): +3: 1 unique blocks of recalibration info detected. +3: Loading systematic error contexts. 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 0.11 sec - 3/10 Test #7: tvcutils_prepare_hotspots_call ................... Passed 0.09 sec - 4/10 Test #8: tvcutils_validate_bed_call ....................... Passed 0.08 sec - 5/10 Test #9: tvcutils_unify_vcf_call .......................... Passed 0.06 sec - 6/10 Test #10: tvcassembly_call ................................. Passed 0.05 sec -5: Loaded. -2: Loaded. +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: Loaded. 4: Loaded. +2: Loaded. +5: Loaded. +4: +4: +4: [tvc] Normal termination. Processing time: 1 seconds. +3: Recalibration model: suppressed +3: +3: +3: [tvc] Normal termination. Processing time: 1 seconds. 2: Recalibration model: suppressed 2: 2: @@ -1972,26 +2015,19 @@ 5: 5: 5: [tvc] Normal termination. Processing time: 1 seconds. -3: Recalibration model: suppressed -3: -3: -3: [tvc] Normal termination. Processing time: 1 seconds. - 7/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 1.54 sec - 8/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.49 sec - 9/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 1.60 sec -4: -4: -4: [tvc] Normal termination. Processing time: 1 seconds. -10/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 1.81 sec + 7/10 Test #3: tvc_test_1_thread_sse_off ........................ Passed 1.19 sec + 8/10 Test #4: tvc_test_4_threads_sse_on_with_parameter_file .... Passed 1.19 sec + 9/10 Test #2: tvc_test_1_thread_sse_on ......................... Passed 1.21 sec +10/10 Test #5: tvc_test_4_threads_sse_off_with_parameter_file ... Passed 1.26 sec 100% tests passed, 0 tests failed out of 10 -Total Test time (real) = 1.88 sec +Total Test time (real) = 1.27 sec make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install --destdir=debian/tvc/ - cd obj-i686-linux-gnu && make -j22 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j10 install DESTDIR=/build/reproducible-path/tvc-5.0.3\+git20151221.80e144e\+dfsg/debian/tvc AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg -B/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -2007,30 +2043,30 @@ -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/bin/variant_caller_pipeline.py -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/targetseq_germline_lowstringency_p1_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_somatic_lowstringency_p1_parameters.json --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ocp_somatic_lowstringency_pgm_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/pgx4_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_somatic_lowstringency_pgm_parameters.json --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseqexome_germline_lowstringency_p1_parameters.json +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/pluginMedia/parameter_sets/ampliseq_germline_lowstringency_pgm_parameters.json -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/motifset.txt +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/sse/ampliseqexome_germline_p1_hiq_motifset.txt -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1 --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_merged_plain.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/TSVC_variants.vcf --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta.fai +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/expected/small_variants.vcf -- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.dict --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_unmerged_detail.bed --- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test_original.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bam.bai +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/test.bed +-- Installing: /build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/debian/tvc/usr/share/TVC/examples/example1/reference.fasta make[1]: Leaving directory '/build/reproducible-path/tvc-5.0.3+git20151221.80e144e+dfsg/obj-i686-linux-gnu' dh_installdocs dh_installchangelogs @@ -2045,13 +2081,13 @@ 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) +dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/tvc/usr/bin/tvc debian/tvc/usr/bin/tvcutils 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_i386.deb'. dpkg-deb: building package 'tvc' in '../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.deb'. +dpkg-deb: building package 'tvc-dbgsym' in '../tvc-dbgsym_5.0.3+git20151221.80e144e+dfsg-5_i386.deb'. dpkg-genbuildinfo --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo dpkg-genchanges --build=binary -O../tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -2059,12 +2095,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/21070/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/21070/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/119334 and its subdirectories -I: Current time: Thu Dec 25 11:03:25 -12 2025 -I: pbuilder-time-stamp: 1766703805 +I: removing directory /srv/workspace/pbuilder/21070 and its subdirectories +I: Current time: Sat Nov 23 06:42:20 +14 2024 +I: pbuilder-time-stamp: 1732293740 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5.diff: 92.6% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5.diff.gz b2/build.log: 90.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 90.2% -- replaced with stdout Fri Nov 22 16:42:22 UTC 2024 I: diffoscope 283 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_tvc_trixie_i386_1732293742 + touch /var/log/reproducible-builds/diffoscope_stamp_tvc_trixie_i386_1732293742 + RESULT=0 + systemd-run '--description=diffoscope on tvc/5.0.3+git20151221.80e144e+dfsg-5 in trixie/i386' --slice=rb-build-diffoscope.slice -u rb-diffoscope-i386_11-33961 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR --run-session -c jenkins-reproducible-trixie-diffoscope-d548b25a-eb89-4175-99a6-73967a48046b -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/dbd-tmp-Vjokjdy ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/tvc_5.0.3+git20151221.80e144e+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/tvc_5.0.3+git20151221.80e144e+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/tvc_5.0.3+git20151221.80e144e+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes' + false + set +x Running as unit: rb-diffoscope-i386_11-33961.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/tvc_5.0.3+git20151221.80e144e+dfsg-5.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/tvc_5.0.3+git20151221.80e144e+dfsg-5.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/tvc_5.0.3+git20151221.80e144e+dfsg-5.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes /srv/reproducible-results/rbuild-debian/r-b-build.CuoiAxuR/b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 0.468s) 0.468s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.128s) 0.128s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 788ms CPU time consumed: 784ms _ | |___ _____ | __\ \ / / __| | |_ \ V / (__ \__| \_/ \___| Fri Nov 22 16:42:23 UTC 2024 I: diffoscope 283 found no differences in the changes files, and a .buildinfo file also exists. Fri Nov 22 16:42:23 UTC 2024 I: tvc from trixie built successfully and reproducibly on i386. INSERT 0 1 INSERT 0 1 DELETE 1 [2024-11-22 16:42:24] INFO: Starting at 2024-11-22 16:42:24.608467 [2024-11-22 16:42:24] INFO: Generating the pages of 1 package(s) [2024-11-22 16:42:25] CRITICAL: https://tests.reproducible-builds.org/debian/trixie/i386/tvc didn't produce a buildlog, even though it has been built. [2024-11-22 16:42:25] INFO: Finished at 2024-11-22 16:42:25.205588, took: 0:00:00.597129 Fri Nov 22 16:42:25 UTC 2024 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/trixie/i386/tvc.html Fri Nov 22 16:42:25 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Nov 22 16:42:25 UTC 2024 I: Submitting 12K b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc https://buildinfo.debian.net/db829895b206cdbcce5c34ddb7000ac9599b437a/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386 Fri Nov 22 16:42:26 UTC 2024 I: Submitting 12K b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc https://buildinfo.debian.net/49ea31a5c9b2f1d1111108c67c715f14a5c4f7ad/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386 Fri Nov 22 16:42:29 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Nov 22 16:42:29 UTC 2024 I: Done submitting .buildinfo files. Fri Nov 22 16:42:29 UTC 2024 I: Removing signed tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc files: removed './b1/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc' removed './b2/tvc_5.0.3+git20151221.80e144e+dfsg-5_i386.buildinfo.asc' 1732293749 i386 trixie tvc Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5.rbuild.log: 89.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/trixie/i386/tvc_5.0.3+git20151221.80e144e+dfsg-5.rbuild.log.gz [2024-11-22 16:42:29] INFO: Starting at 2024-11-22 16:42:29.382273 [2024-11-22 16:42:29] INFO: Generating the pages of 1 package(s) [2024-11-22 16:42:29] INFO: Finished at 2024-11-22 16:42:29.860896, took: 0:00:00.478629 All cleanup done. Fri Nov 22 16:42:29 UTC 2024 - total duration: 0h 4m 24s. Fri Nov 22 16:42:29 UTC 2024 - reproducible_build.sh stopped running as /tmp/jenkins-script-YlVlQqkR, removing. Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 4min 30.433s CPU time consumed: 7.613s