Diff of the two buildlogs: -- --- b1/build.log 2024-03-26 02:56:51.891805434 +0000 +++ b2/build.log 2024-03-26 03:16:02.426710613 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Mar 25 14:30:53 -12 2024 -I: pbuilder-time-stamp: 1711420253 +I: Current time: Mon Apr 28 23:20:05 +14 2025 +I: pbuilder-time-stamp: 1745832005 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -31,54 +31,86 @@ dpkg-source: info: applying py3 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/60059/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/33246/tmp/hooks/D01_modify_environment starting +debug: Running on ionos6-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 Apr 28 09:20 /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/33246/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/33246/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=8 ' - 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]="21" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.21(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=21 ' + 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='bd1e44180e234e92924edc04df4e48cb' - 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='60059' - PS1='# ' - PS2='> ' + INVOCATION_ID=d7ca2c7c4cce4f079cdbea4dd8486b88 + 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=33246 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.kBpN1lkm/pbuilderrc_I9UN --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.kBpN1lkm/b1 --logfile b1/build.log racon_1.5.0-3.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://78.137.99.97:3128' + 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.kBpN1lkm/pbuilderrc_N6Or --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.kBpN1lkm/b2 --logfile b2/build.log racon_1.5.0-3.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://85.184.249.68:3128 I: uname -a - Linux ionos2-i386 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Mar 25 11:27 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/60059/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 25 17:47 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/33246/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -191,7 +223,7 @@ Get: 59 http://deb.debian.org/debian trixie/main i386 libspoa-dev i386 4.1.4-1 [9396 B] Get: 60 http://deb.debian.org/debian trixie/main i386 libthread-pool-dev i386 4.0.0-2 [7296 B] Get: 61 http://deb.debian.org/debian trixie/main i386 rampler i386 2.1.1-1 [22.5 kB] -Fetched 38.6 MB in 1s (48.5 MB/s) +Fetched 38.6 MB in 0s (82.5 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 ... 19816 files and directories currently installed.) @@ -450,7 +482,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/racon-1.5.0/ && 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 > ../racon_1.5.0-3_source.changes +I: user script /srv/workspace/pbuilder/33246/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/33246/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/racon-1.5.0/ && 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 > ../racon_1.5.0-3_source.changes dpkg-buildpackage: info: source package racon dpkg-buildpackage: info: source version 1.5.0-3 dpkg-buildpackage: info: source distribution unstable @@ -476,7 +512,7 @@ -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done --- Configuring done (1.1s) +-- Configuring done (0.8s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -491,7 +527,7 @@ sed -i 's/-lpthread/-pthread/' obj-*/CMakeFiles/racon_test.dir/link.txt make[1]: Leaving directory '/build/reproducible-path/racon-1.5.0' dh_auto_build -O--buildsystem=cmake - cd obj-i686-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j21 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/racon-1.5.0 -B/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -504,22 +540,15 @@ make -f CMakeFiles/racon.dir/build.make CMakeFiles/racon.dir/build make[3]: Entering directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' [ 10%] Building CXX object CMakeFiles/racon.dir/src/logger.cpp.o -/usr/bin/c++ -I/build/reproducible-path/racon-1.5.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -pthread -MD -MT CMakeFiles/racon.dir/src/logger.cpp.o -MF CMakeFiles/racon.dir/src/logger.cpp.o.d -o CMakeFiles/racon.dir/src/logger.cpp.o -c /build/reproducible-path/racon-1.5.0/src/logger.cpp [ 20%] Building CXX object CMakeFiles/racon.dir/src/polisher.cpp.o [ 30%] Building CXX object CMakeFiles/racon.dir/src/overlap.cpp.o +/usr/bin/c++ -I/build/reproducible-path/racon-1.5.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -pthread -MD -MT CMakeFiles/racon.dir/src/logger.cpp.o -MF CMakeFiles/racon.dir/src/logger.cpp.o.d -o CMakeFiles/racon.dir/src/logger.cpp.o -c /build/reproducible-path/racon-1.5.0/src/logger.cpp /usr/bin/c++ -I/build/reproducible-path/racon-1.5.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -pthread -MD -MT CMakeFiles/racon.dir/src/polisher.cpp.o -MF CMakeFiles/racon.dir/src/polisher.cpp.o.d -o CMakeFiles/racon.dir/src/polisher.cpp.o -c /build/reproducible-path/racon-1.5.0/src/polisher.cpp /usr/bin/c++ -I/build/reproducible-path/racon-1.5.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -pthread -MD -MT CMakeFiles/racon.dir/src/overlap.cpp.o -MF CMakeFiles/racon.dir/src/overlap.cpp.o.d -o CMakeFiles/racon.dir/src/overlap.cpp.o -c /build/reproducible-path/racon-1.5.0/src/overlap.cpp [ 40%] Building CXX object CMakeFiles/racon.dir/src/sequence.cpp.o /usr/bin/c++ -I/build/reproducible-path/racon-1.5.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -pthread -MD -MT CMakeFiles/racon.dir/src/sequence.cpp.o -MF CMakeFiles/racon.dir/src/sequence.cpp.o.d -o CMakeFiles/racon.dir/src/sequence.cpp.o -c /build/reproducible-path/racon-1.5.0/src/sequence.cpp [ 50%] Building CXX object CMakeFiles/racon.dir/src/window.cpp.o /usr/bin/c++ -I/build/reproducible-path/racon-1.5.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -pthread -MD -MT CMakeFiles/racon.dir/src/window.cpp.o -MF CMakeFiles/racon.dir/src/window.cpp.o.d -o CMakeFiles/racon.dir/src/window.cpp.o -c /build/reproducible-path/racon-1.5.0/src/window.cpp -/build/reproducible-path/racon-1.5.0/src/window.cpp: In member function 'bool racon::Window::generate_consensus(std::shared_ptr, bool)': -/build/reproducible-path/racon-1.5.0/src/window.cpp:142:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] - 142 | "contig %lu might be chimeric in window %u!\n", id_, rank_); - | ~~^ ~~~ - | | | - | long unsigned int uint64_t {aka long long unsigned int} - | %llu /build/reproducible-path/racon-1.5.0/src/overlap.cpp: In member function 'virtual void racon::Overlap::align_overlaps(const char*, uint32_t, const char*, uint32_t)': /build/reproducible-path/racon-1.5.0/src/overlap.cpp:219:48: warning: format '%zu' expects argument of type 'size_t', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] 219 | "edlib unable to align pair (%zu x %zu)!\n", q_id_, t_id_); @@ -533,6 +562,13 @@ | | | | unsigned int uint64_t {aka long long unsigned int} | %llu +/build/reproducible-path/racon-1.5.0/src/window.cpp: In member function 'bool racon::Window::generate_consensus(std::shared_ptr, bool)': +/build/reproducible-path/racon-1.5.0/src/window.cpp:142:27: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'uint64_t' {aka 'long long unsigned int'} [-Wformat=] + 142 | "contig %lu might be chimeric in window %u!\n", id_, rank_); + | ~~^ ~~~ + | | | + | long unsigned int uint64_t {aka long long unsigned int} + | %llu [ 60%] Linking CXX static library lib/libracon.a /usr/bin/cmake -P CMakeFiles/racon.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/racon.dir/link.txt --verbose=1 @@ -543,19 +579,19 @@ make -f CMakeFiles/racon_exe.dir/build.make CMakeFiles/racon_exe.dir/depend make -f CMakeFiles/racon_test.dir/build.make CMakeFiles/racon_test.dir/depend make[3]: Entering directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' -cd /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/racon-1.5.0 /build/reproducible-path/racon-1.5.0 /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu/CMakeFiles/racon_test.dir/DependInfo.cmake "--color=" -make[3]: Entering directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' cd /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/racon-1.5.0 /build/reproducible-path/racon-1.5.0 /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu/CMakeFiles/racon_exe.dir/DependInfo.cmake "--color=" -make[3]: Leaving directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' -make -f CMakeFiles/racon_test.dir/build.make CMakeFiles/racon_test.dir/build make[3]: Entering directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' -[ 70%] Building CXX object CMakeFiles/racon_test.dir/test/racon_test.cpp.o -/usr/bin/c++ -DTEST_DATA=\"/build/reproducible-path/racon-1.5.0/test/data/\" -I/build/reproducible-path/racon-1.5.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++14 -DGTEST_HAS_PTHREAD=1 -MD -MT CMakeFiles/racon_test.dir/test/racon_test.cpp.o -MF CMakeFiles/racon_test.dir/test/racon_test.cpp.o.d -o CMakeFiles/racon_test.dir/test/racon_test.cpp.o -c /build/reproducible-path/racon-1.5.0/test/racon_test.cpp +cd /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/racon-1.5.0 /build/reproducible-path/racon-1.5.0 /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu /build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu/CMakeFiles/racon_test.dir/DependInfo.cmake "--color=" +make[3]: Leaving directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' make -f CMakeFiles/racon_exe.dir/build.make CMakeFiles/racon_exe.dir/build +make -f CMakeFiles/racon_test.dir/build.make CMakeFiles/racon_test.dir/build +make[3]: Entering directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' -[ 80%] Building CXX object CMakeFiles/racon_exe.dir/src/main.cpp.o +[ 70%] Building CXX object CMakeFiles/racon_exe.dir/src/main.cpp.o +[ 80%] Building CXX object CMakeFiles/racon_test.dir/test/racon_test.cpp.o /usr/bin/c++ -DVERSION=\"1.5.0\" -I/build/reproducible-path/racon-1.5.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++11 -MD -MT CMakeFiles/racon_exe.dir/src/main.cpp.o -MF CMakeFiles/racon_exe.dir/src/main.cpp.o.d -o CMakeFiles/racon_exe.dir/src/main.cpp.o -c /build/reproducible-path/racon-1.5.0/src/main.cpp +/usr/bin/c++ -DTEST_DATA=\"/build/reproducible-path/racon-1.5.0/test/data/\" -I/build/reproducible-path/racon-1.5.0/src -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -std=c++14 -DGTEST_HAS_PTHREAD=1 -MD -MT CMakeFiles/racon_test.dir/test/racon_test.cpp.o -MF CMakeFiles/racon_test.dir/test/racon_test.cpp.o.d -o CMakeFiles/racon_test.dir/test/racon_test.cpp.o -c /build/reproducible-path/racon-1.5.0/test/racon_test.cpp [ 90%] Linking CXX executable bin/racon /usr/bin/cmake -E cmake_link_script CMakeFiles/racon_exe.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/racon-1.5.0=. -fstack-protector-strong -Wformat -Werror=format-security -ffloat-store -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -pedantic -Wl,-z,relro -Wl,-z,now CMakeFiles/racon_exe.dir/src/main.cpp.o -o bin/racon lib/libracon.a -ledlib -lspoa -lpthread -lz @@ -577,119 +613,119 @@ [----------] Global test environment set-up. [----------] 5 tests from RaconInitializeTest [ RUN ] RaconInitializeTest.PolisherTypeError -[ OK ] RaconInitializeTest.PolisherTypeError (16 ms) +[ OK ] RaconInitializeTest.PolisherTypeError (0 ms) [ RUN ] RaconInitializeTest.WindowLengthError -[ OK ] RaconInitializeTest.WindowLengthError (3 ms) +[ OK ] RaconInitializeTest.WindowLengthError (1 ms) [ RUN ] RaconInitializeTest.SequencesPathExtensionError -[ OK ] RaconInitializeTest.SequencesPathExtensionError (12 ms) +[ OK ] RaconInitializeTest.SequencesPathExtensionError (1 ms) [ RUN ] RaconInitializeTest.OverlapsPathExtensionError -[ OK ] RaconInitializeTest.OverlapsPathExtensionError (19 ms) +[ OK ] RaconInitializeTest.OverlapsPathExtensionError (2 ms) [ RUN ] RaconInitializeTest.TargetPathExtensionError -[ OK ] RaconInitializeTest.TargetPathExtensionError (19 ms) -[----------] 5 tests from RaconInitializeTest (72 ms total) +[ OK ] RaconInitializeTest.TargetPathExtensionError (2 ms) +[----------] 5 tests from RaconInitializeTest (9 ms total) [----------] 10 tests from RaconPolishingTest [ RUN ] RaconPolishingTest.ConsensusWithQualities -[racon::Polisher::initialize] loaded target sequences 0.002388 s -[racon::Polisher::initialize] loaded sequences 0.106597 s -[racon::Polisher::initialize] loaded overlaps 0.004415 s -[racon::Polisher::initialize] aligning overlaps [=> ] 0.173177 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.257134 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.349166 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.429114 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.521139 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.609139 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.817138 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.925116 s [racon::Polisher::initialize] aligning overlaps [=========> ] 1.013114 s [racon::Polisher::initialize] aligning overlaps [==========> ] 1.085115 s [racon::Polisher::initialize] aligning overlaps [===========> ] 1.193135 s [racon::Polisher::initialize] aligning overlaps [============> ] 1.233131 s [racon::Polisher::initialize] aligning overlaps [=============> ] 1.269146 s [racon::Polisher::initialize] aligning overlaps [==============> ] 1.269281 s [racon::Polisher::initialize] aligning overlaps [===============> ] 1.285140 s [racon::Polisher::initialize] aligning overlaps [================> ] 1.293122 s [racon::Polisher::initialize] aligning overlaps [=================> ] 1.297049 s [racon::Polisher::initialize] aligning overlaps [==================> ] 1.357172 s [racon::Polisher::initialize] aligning overlaps [===================>] 1.357307 s [racon::Polisher::initialize] aligning overlaps [====================] 1.373186 s -[racon::Polisher::initialize] transformed data into windows 0.111769 s -[racon::Polisher::polish] generating consensus [=> ] 0.932006 s [racon::Polisher::polish] generating consensus [==> ] 1.624044 s [racon::Polisher::polish] generating consensus [===> ] 2.128776 s [racon::Polisher::polish] generating consensus [====> ] 2.496102 s [racon::Polisher::polish] generating consensus [=====> ] 2.792054 s [racon::Polisher::polish] generating consensus [======> ] 3.036140 s [racon::Polisher::polish] generating consensus [=======> ] 3.252616 s [racon::Polisher::polish] generating consensus [========> ] 3.716094 s [racon::Polisher::polish] generating consensus [=========> ] 4.488270 s [racon::Polisher::polish] generating consensus [==========> ] 5.343966 s [racon::Polisher::polish] generating consensus [===========> ] 6.195862 s [racon::Polisher::polish] generating consensus [============> ] 6.919860 s [racon::Polisher::polish] generating consensus [=============> ] 8.783912 s [racon::Polisher::polish] generating consensus [==============> ] 9.975869 s [racon::Polisher::polish] generating consensus [===============> ] 10.711892 s [racon::Polisher::polish] generating consensus [================> ] 11.543882 s [racon::Polisher::polish] generating consensus [=================> ] 12.499862 s [racon::Polisher::polish] generating consensus [==================> ] 13.023857 s [racon::Polisher::polish] generating consensus [===================>] 13.708342 s [racon::Polisher::polish] generating consensus [====================] 15.808773 s -[racon::Polisher::] total = 17.452825 s -[ OK ] RaconPolishingTest.ConsensusWithQualities (17496 ms) +[racon::Polisher::initialize] loaded target sequences 0.001060 s +[racon::Polisher::initialize] loaded sequences 0.043927 s +[racon::Polisher::initialize] loaded overlaps 0.000671 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.066807 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.104648 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.153012 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.187520 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.233394 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.271486 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.368931 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.419052 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.457208 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.493135 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.540629 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.582237 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.617766 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.626738 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.632952 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.649546 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.652668 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.653097 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.668452 s [racon::Polisher::initialize] aligning overlaps [====================] 0.674406 s +[racon::Polisher::initialize] transformed data into windows 0.021572 s +[racon::Polisher::polish] generating consensus [=> ] 0.475259 s [racon::Polisher::polish] generating consensus [==> ] 0.919916 s [racon::Polisher::polish] generating consensus [===> ] 1.351519 s [racon::Polisher::polish] generating consensus [====> ] 1.720224 s [racon::Polisher::polish] generating consensus [=====> ] 1.964387 s [racon::Polisher::polish] generating consensus [======> ] 2.183691 s [racon::Polisher::polish] generating consensus [=======> ] 2.366472 s [racon::Polisher::polish] generating consensus [========> ] 2.577869 s [racon::Polisher::polish] generating consensus [=========> ] 2.966279 s [racon::Polisher::polish] generating consensus [==========> ] 3.363845 s [racon::Polisher::polish] generating consensus [===========> ] 4.084197 s [racon::Polisher::polish] generating consensus [============> ] 4.992186 s [racon::Polisher::polish] generating consensus [=============> ] 6.288600 s [racon::Polisher::polish] generating consensus [==============> ] 7.664651 s [racon::Polisher::polish] generating consensus [===============> ] 8.512642 s [racon::Polisher::polish] generating consensus [================> ] 9.136188 s [racon::Polisher::polish] generating consensus [=================> ] 9.868617 s [racon::Polisher::polish] generating consensus [==================> ] 10.304615 s [racon::Polisher::polish] generating consensus [===================>] 10.888598 s [racon::Polisher::polish] generating consensus [====================] 13.157770 s +[racon::Polisher::] total = 13.941316 s +[ OK ] RaconPolishingTest.ConsensusWithQualities (13956 ms) [ RUN ] RaconPolishingTest.ConsensusWithoutQualities -[racon::Polisher::initialize] loaded target sequences 0.001907 s -[racon::Polisher::initialize] loaded sequences 0.033135 s -[racon::Polisher::initialize] loaded overlaps 0.000581 s -[racon::Polisher::initialize] aligning overlaps [=> ] 0.104629 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.197959 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.297892 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.381707 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.417646 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.429712 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.465748 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.497641 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.717823 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.805827 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.841723 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.917836 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.997775 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.998256 s [racon::Polisher::initialize] aligning overlaps [===============> ] 1.049846 s [racon::Polisher::initialize] aligning overlaps [================> ] 1.065796 s [racon::Polisher::initialize] aligning overlaps [=================> ] 1.170732 s [racon::Polisher::initialize] aligning overlaps [==================> ] 1.224588 s [racon::Polisher::initialize] aligning overlaps [===================>] 1.224762 s [racon::Polisher::initialize] aligning overlaps [====================] 1.238992 s -[racon::Polisher::initialize] transformed data into windows 0.000821 s -[racon::Polisher::polish] generating consensus [=> ] 1.277517 s [racon::Polisher::polish] generating consensus [==> ] 2.449765 s [racon::Polisher::polish] generating consensus [===> ] 2.965799 s [racon::Polisher::polish] generating consensus [====> ] 3.521978 s [racon::Polisher::polish] generating consensus [=====> ] 3.845935 s [racon::Polisher::polish] generating consensus [======> ] 4.265073 s [racon::Polisher::polish] generating consensus [=======> ] 4.585901 s [racon::Polisher::polish] generating consensus [========> ] 4.941955 s [racon::Polisher::polish] generating consensus [=========> ] 5.489484 s [racon::Polisher::polish] generating consensus [==========> ] 6.313772 s [racon::Polisher::polish] generating consensus [===========> ] 7.333478 s [racon::Polisher::polish] generating consensus [============> ] 8.405916 s [racon::Polisher::polish] generating consensus [=============> ] 10.025506 s [racon::Polisher::polish] generating consensus [==============> ] 11.125481 s [racon::Polisher::polish] generating consensus [===============> ] 12.309004 s [racon::Polisher::polish] generating consensus [================> ] 13.581552 s [racon::Polisher::polish] generating consensus [=================> ] 14.629521 s [racon::Polisher::polish] generating consensus [==================> ] 15.281824 s [racon::Polisher::polish] generating consensus [===================>] 16.165887 s [racon::Polisher::polish] generating consensus [====================] 20.166056 s -[racon::Polisher::] total = 21.497522 s -[ OK ] RaconPolishingTest.ConsensusWithoutQualities (21524 ms) +[racon::Polisher::initialize] loaded target sequences 0.001008 s +[racon::Polisher::initialize] loaded sequences 0.026677 s +[racon::Polisher::initialize] loaded overlaps 0.000673 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.077122 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.109002 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.137112 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.173103 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.209122 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.242028 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.328662 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.370387 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.404997 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.437001 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.476867 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.512923 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.557099 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.573448 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.598382 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.645482 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.665483 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.697467 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.752722 s [racon::Polisher::initialize] aligning overlaps [====================] 0.797215 s +[racon::Polisher::initialize] transformed data into windows 0.000905 s +[racon::Polisher::polish] generating consensus [=> ] 0.687423 s [racon::Polisher::polish] generating consensus [==> ] 1.494285 s [racon::Polisher::polish] generating consensus [===> ] 2.058173 s [racon::Polisher::polish] generating consensus [====> ] 2.534195 s [racon::Polisher::polish] generating consensus [=====> ] 2.825025 s [racon::Polisher::polish] generating consensus [======> ] 3.157689 s [racon::Polisher::polish] generating consensus [=======> ] 3.479959 s [racon::Polisher::polish] generating consensus [========> ] 3.834643 s [racon::Polisher::polish] generating consensus [=========> ] 4.366649 s [racon::Polisher::polish] generating consensus [==========> ] 5.170161 s [racon::Polisher::polish] generating consensus [===========> ] 6.054162 s [racon::Polisher::polish] generating consensus [============> ] 7.082581 s [racon::Polisher::polish] generating consensus [=============> ] 8.578581 s [racon::Polisher::polish] generating consensus [==============> ] 9.682160 s [racon::Polisher::polish] generating consensus [===============> ] 10.774161 s [racon::Polisher::polish] generating consensus [================> ] 11.806164 s [racon::Polisher::polish] generating consensus [=================> ] 12.786202 s [racon::Polisher::polish] generating consensus [==================> ] 13.394193 s [racon::Polisher::polish] generating consensus [===================>] 14.086168 s [racon::Polisher::polish] generating consensus [====================] 18.446154 s +[racon::Polisher::] total = 19.310792 s +[ OK ] RaconPolishingTest.ConsensusWithoutQualities (19330 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments -[racon::Polisher::initialize] loaded target sequences 0.000876 s -[racon::Polisher::initialize] loaded sequences 0.063028 s -[racon::Polisher::initialize] loaded overlaps 0.054106 s -[racon::Polisher::initialize] aligning overlaps [=> ] 0.016273 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.016405 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.016525 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.016643 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.016760 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.016897 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.017014 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.017131 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.017248 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.017366 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.017482 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.017596 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.017711 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.017827 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.017942 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.022603 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.022725 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.022842 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.022964 s [racon::Polisher::initialize] aligning overlaps [====================] 0.023081 s -[racon::Polisher::initialize] transformed data into windows 0.087781 s -[racon::Polisher::polish] generating consensus [=> ] 0.745209 s [racon::Polisher::polish] generating consensus [==> ] 1.325202 s [racon::Polisher::polish] generating consensus [===> ] 2.041175 s [racon::Polisher::polish] generating consensus [====> ] 2.461223 s [racon::Polisher::polish] generating consensus [=====> ] 2.645204 s [racon::Polisher::polish] generating consensus [======> ] 2.841473 s [racon::Polisher::polish] generating consensus [=======> ] 3.165539 s [racon::Polisher::polish] generating consensus [========> ] 3.457622 s [racon::Polisher::polish] generating consensus [=========> ] 3.685511 s [racon::Polisher::polish] generating consensus [==========> ] 4.256556 s [racon::Polisher::polish] generating consensus [===========> ] 5.061517 s [racon::Polisher::polish] generating consensus [============> ] 6.025526 s [racon::Polisher::polish] generating consensus [=============> ] 7.081087 s [racon::Polisher::polish] generating consensus [==============> ] 8.529093 s [racon::Polisher::polish] generating consensus [===============> ] 9.637082 s [racon::Polisher::polish] generating consensus [================> ] 10.373117 s [racon::Polisher::polish] generating consensus [=================> ] 11.253081 s [racon::Polisher::polish] generating consensus [==================> ] 11.753086 s [racon::Polisher::polish] generating consensus [===================>] 12.221071 s [racon::Polisher::polish] generating consensus [====================] 14.146083 s -[racon::Polisher::] total = 14.430012 s -[ OK ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments (14459 ms) +[racon::Polisher::initialize] loaded target sequences 0.001102 s +[racon::Polisher::initialize] loaded sequences 0.056292 s +[racon::Polisher::initialize] loaded overlaps 0.032212 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.010022 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.010633 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.011147 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.011622 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.012078 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.012526 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.012988 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.013433 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.013865 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.014336 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.014863 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.015498 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.016140 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.016679 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.017116 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.017537 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.017977 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.018419 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.018849 s [racon::Polisher::initialize] aligning overlaps [====================] 0.019288 s +[racon::Polisher::initialize] transformed data into windows 0.021553 s +[racon::Polisher::polish] generating consensus [=> ] 0.678305 s [racon::Polisher::polish] generating consensus [==> ] 1.306302 s [racon::Polisher::polish] generating consensus [===> ] 1.922294 s [racon::Polisher::polish] generating consensus [====> ] 2.366760 s [racon::Polisher::polish] generating consensus [=====> ] 2.550606 s [racon::Polisher::polish] generating consensus [======> ] 2.758650 s [racon::Polisher::polish] generating consensus [=======> ] 3.014647 s [racon::Polisher::polish] generating consensus [========> ] 3.290712 s [racon::Polisher::polish] generating consensus [=========> ] 3.522289 s [racon::Polisher::polish] generating consensus [==========> ] 4.142293 s [racon::Polisher::polish] generating consensus [===========> ] 4.810736 s [racon::Polisher::polish] generating consensus [============> ] 5.718701 s [racon::Polisher::polish] generating consensus [=============> ] 6.846303 s [racon::Polisher::polish] generating consensus [==============> ] 8.074763 s [racon::Polisher::polish] generating consensus [===============> ] 9.124769 s [racon::Polisher::polish] generating consensus [================> ] 9.814850 s [racon::Polisher::polish] generating consensus [=================> ] 10.670694 s [racon::Polisher::polish] generating consensus [==================> ] 11.150307 s [racon::Polisher::polish] generating consensus [===================>] 11.602304 s [racon::Polisher::polish] generating consensus [====================] 13.421028 s +[racon::Polisher::] total = 13.594812 s +[ OK ] RaconPolishingTest.ConsensusWithQualitiesAndAlignments (13615 ms) [ RUN ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments -[racon::Polisher::initialize] loaded target sequences 0.001214 s -[racon::Polisher::initialize] loaded sequences 0.029469 s -[racon::Polisher::initialize] loaded overlaps 0.035179 s -[racon::Polisher::initialize] aligning overlaps [=> ] 0.018626 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.019342 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.019955 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.020552 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.021138 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.021742 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.022349 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.022882 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.023410 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.023931 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.024496 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.025038 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.025638 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.026271 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.026899 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.027494 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.028210 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.028742 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.029252 s [racon::Polisher::initialize] aligning overlaps [====================] 0.029769 s -[racon::Polisher::initialize] transformed data into windows 0.001104 s -[racon::Polisher::polish] generating consensus [=> ] 0.699218 s [racon::Polisher::polish] generating consensus [==> ] 1.451895 s [racon::Polisher::polish] generating consensus [===> ] 2.155260 s [racon::Polisher::polish] generating consensus [====> ] 2.675195 s [racon::Polisher::polish] generating consensus [=====> ] 2.999301 s [racon::Polisher::polish] generating consensus [======> ] 3.295143 s [racon::Polisher::polish] generating consensus [=======> ] 3.615203 s [racon::Polisher::polish] generating consensus [========> ] 4.055220 s [racon::Polisher::polish] generating consensus [=========> ] 4.479050 s [racon::Polisher::polish] generating consensus [==========> ] 5.151117 s [racon::Polisher::polish] generating consensus [===========> ] 6.023063 s [racon::Polisher::polish] generating consensus [============> ] 7.115136 s [racon::Polisher::polish] generating consensus [=============> ] 8.514723 s [racon::Polisher::polish] generating consensus [==============> ] 9.935219 s [racon::Polisher::polish] generating consensus [===============> ] 11.134718 s [racon::Polisher::polish] generating consensus [================> ] 12.239232 s [racon::Polisher::polish] generating consensus [=================> ] 13.126713 s [racon::Polisher::polish] generating consensus [==================> ] 13.638715 s [racon::Polisher::polish] generating consensus [===================>] 14.202698 s [racon::Polisher::polish] generating consensus [====================] 17.485959 s -[racon::Polisher::] total = 17.623345 s -[ OK ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments (17645 ms) +[racon::Polisher::initialize] loaded target sequences 0.001067 s +[racon::Polisher::initialize] loaded sequences 0.026592 s +[racon::Polisher::initialize] loaded overlaps 0.030356 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.012524 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.013172 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.013732 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.014177 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.014326 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.014454 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.014933 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.015424 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.015918 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.016420 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.016891 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.017526 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.018085 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.018708 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.019204 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.019650 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.020101 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.020541 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.020997 s [racon::Polisher::initialize] aligning overlaps [====================] 0.021459 s +[racon::Polisher::initialize] transformed data into windows 0.000933 s +[racon::Polisher::polish] generating consensus [=> ] 0.763397 s [racon::Polisher::polish] generating consensus [==> ] 1.555406 s [racon::Polisher::polish] generating consensus [===> ] 2.179969 s [racon::Polisher::polish] generating consensus [====> ] 2.567530 s [racon::Polisher::polish] generating consensus [=====> ] 2.787395 s [racon::Polisher::polish] generating consensus [======> ] 3.111390 s [racon::Polisher::polish] generating consensus [=======> ] 3.411844 s [racon::Polisher::polish] generating consensus [========> ] 4.014789 s [racon::Polisher::polish] generating consensus [=========> ] 4.383396 s [racon::Polisher::polish] generating consensus [==========> ] 5.139399 s [racon::Polisher::polish] generating consensus [===========> ] 5.903397 s [racon::Polisher::polish] generating consensus [============> ] 6.927410 s [racon::Polisher::polish] generating consensus [=============> ] 8.447413 s [racon::Polisher::polish] generating consensus [==============> ] 9.727408 s [racon::Polisher::polish] generating consensus [===============> ] 10.839395 s [racon::Polisher::polish] generating consensus [================> ] 11.771908 s [racon::Polisher::polish] generating consensus [=================> ] 12.531849 s [racon::Polisher::polish] generating consensus [==================> ] 13.079395 s [racon::Polisher::polish] generating consensus [===================>] 13.707847 s [racon::Polisher::polish] generating consensus [====================] 16.653037 s +[racon::Polisher::] total = 16.754567 s +[ OK ] RaconPolishingTest.ConsensusWithoutQualitiesAndWithAlignments (16772 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow -[racon::Polisher::initialize] loaded target sequences 0.000871 s -[racon::Polisher::initialize] loaded sequences 0.054388 s -[racon::Polisher::initialize] loaded overlaps 0.000461 s -[racon::Polisher::initialize] aligning overlaps [=> ] 0.153826 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.253853 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.381832 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.490127 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.534113 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.574115 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.670051 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.718130 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.758126 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.794105 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.838100 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.882056 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.962058 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.982117 s [racon::Polisher::initialize] aligning overlaps [===============> ] 1.070496 s [racon::Polisher::initialize] aligning overlaps [================> ] 1.110048 s [racon::Polisher::initialize] aligning overlaps [=================> ] 1.170077 s [racon::Polisher::initialize] aligning overlaps [==================> ] 1.206086 s [racon::Polisher::initialize] aligning overlaps [===================>] 1.206716 s [racon::Polisher::initialize] aligning overlaps [====================] 1.234214 s -[racon::Polisher::initialize] transformed data into windows 0.066916 s -[racon::Polisher::polish] generating consensus [=> ] 2.296404 s [racon::Polisher::polish] generating consensus [==> ] 2.297019 s [racon::Polisher::polish] generating consensus [===> ] 4.108299 s [racon::Polisher::polish] generating consensus [====> ] 4.108983 s [racon::Polisher::polish] generating consensus [=====> ] 4.964279 s [racon::Polisher::polish] generating consensus [======> ] 4.964932 s [racon::Polisher::polish] generating consensus [=======> ] 5.788269 s [racon::Polisher::polish] generating consensus [========> ] 5.876334 s [racon::Polisher::polish] generating consensus [=========> ] 7.264266 s [racon::Polisher::polish] generating consensus [==========> ] 8.048368 s [racon::Polisher::polish] generating consensus [===========> ] 9.787921 s [racon::Polisher::polish] generating consensus [============> ] 11.343897 s [racon::Polisher::polish] generating consensus [=============> ] 15.328342 s [racon::Polisher::polish] generating consensus [==============> ] 16.560296 s [racon::Polisher::polish] generating consensus [===============> ] 18.263950 s [racon::Polisher::polish] generating consensus [================> ] 19.463989 s [racon::Polisher::polish] generating consensus [=================> ] 20.844345 s [racon::Polisher::polish] generating consensus [==================> ] 21.924287 s [racon::Polisher::polish] generating consensus [===================>] 22.971921 s [racon::Polisher::polish] generating consensus [====================] 29.123959 s -[racon::Polisher::] total = 30.545704 s -[ OK ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow (30633 ms) +[racon::Polisher::initialize] loaded target sequences 0.000629 s +[racon::Polisher::initialize] loaded sequences 0.041202 s +[racon::Polisher::initialize] loaded overlaps 0.000519 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.055258 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.090504 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.132106 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.176600 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.209761 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.217273 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.294981 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.338381 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.373635 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.404474 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.447667 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.484107 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.528553 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.545232 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.589517 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.623515 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.689880 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.694923 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.725467 s [racon::Polisher::initialize] aligning overlaps [====================] 0.740553 s +[racon::Polisher::initialize] transformed data into windows 0.021402 s +[racon::Polisher::polish] generating consensus [=> ] 2.270444 s [racon::Polisher::polish] generating consensus [==> ] 2.272944 s [racon::Polisher::polish] generating consensus [===> ] 4.303393 s [racon::Polisher::polish] generating consensus [====> ] 4.303437 s [racon::Polisher::polish] generating consensus [=====> ] 5.299827 s [racon::Polisher::polish] generating consensus [======> ] 5.300382 s [racon::Polisher::polish] generating consensus [=======> ] 6.087383 s [racon::Polisher::polish] generating consensus [========> ] 6.087430 s [racon::Polisher::polish] generating consensus [=========> ] 7.559385 s [racon::Polisher::polish] generating consensus [==========> ] 7.823372 s [racon::Polisher::polish] generating consensus [===========> ] 10.307376 s [racon::Polisher::polish] generating consensus [============> ] 10.906725 s [racon::Polisher::polish] generating consensus [=============> ] 14.623653 s [racon::Polisher::polish] generating consensus [==============> ] 15.118305 s [racon::Polisher::polish] generating consensus [===============> ] 17.371381 s [racon::Polisher::polish] generating consensus [================> ] 17.567418 s [racon::Polisher::polish] generating consensus [=================> ] 19.987858 s [racon::Polisher::polish] generating consensus [==================> ] 19.988465 s [racon::Polisher::polish] generating consensus [===================>] 22.019807 s [racon::Polisher::polish] generating consensus [====================] 26.153230 s +[racon::Polisher::] total = 26.986552 s +[ OK ] RaconPolishingTest.ConsensusWithQualitiesLargerWindow (27049 ms) [ RUN ] RaconPolishingTest.ConsensusWithQualitiesEditDistance -[racon::Polisher::initialize] loaded target sequences 0.001136 s -[racon::Polisher::initialize] loaded sequences 0.059056 s -[racon::Polisher::initialize] loaded overlaps 0.000639 s -[racon::Polisher::initialize] aligning overlaps [=> ] 0.224953 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.356858 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.436902 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.544906 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.600909 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.624807 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.672943 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.761043 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.777036 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.813027 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.845158 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.924950 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.952924 s [racon::Polisher::initialize] aligning overlaps [==============> ] 1.040887 s [racon::Polisher::initialize] aligning overlaps [===============> ] 1.140966 s [racon::Polisher::initialize] aligning overlaps [================> ] 1.188941 s [racon::Polisher::initialize] aligning overlaps [=================> ] 1.208994 s [racon::Polisher::initialize] aligning overlaps [==================> ] 1.260907 s [racon::Polisher::initialize] aligning overlaps [===================>] 1.296890 s [racon::Polisher::initialize] aligning overlaps [====================] 1.347513 s -[racon::Polisher::initialize] transformed data into windows 0.063397 s -[racon::Polisher::polish] generating consensus [=> ] 0.941838 s [racon::Polisher::polish] generating consensus [==> ] 1.653811 s [racon::Polisher::polish] generating consensus [===> ] 2.201416 s [racon::Polisher::polish] generating consensus [====> ] 2.649750 s [racon::Polisher::polish] generating consensus [=====> ] 2.829833 s [racon::Polisher::polish] generating consensus [======> ] 3.049825 s [racon::Polisher::polish] generating consensus [=======> ] 3.409850 s [racon::Polisher::polish] generating consensus [========> ] 3.762432 s [racon::Polisher::polish] generating consensus [=========> ] 4.181948 s [racon::Polisher::polish] generating consensus [==========> ] 4.685870 s [racon::Polisher::polish] generating consensus [===========> ] 5.489819 s [racon::Polisher::polish] generating consensus [============> ] 6.101855 s [racon::Polisher::polish] generating consensus [=============> ] 7.285798 s [racon::Polisher::polish] generating consensus [==============> ] 8.173813 s [racon::Polisher::polish] generating consensus [===============> ] 9.289389 s [racon::Polisher::polish] generating consensus [================> ] 10.857444 s [racon::Polisher::polish] generating consensus [=================> ] 11.613449 s [racon::Polisher::polish] generating consensus [==================> ] 12.085394 s [racon::Polisher::polish] generating consensus [===================>] 12.729414 s [racon::Polisher::polish] generating consensus [====================] 14.784695 s -[racon::Polisher::] total = 16.308678 s -[ OK ] RaconPolishingTest.ConsensusWithQualitiesEditDistance (16331 ms) +[racon::Polisher::initialize] loaded target sequences 0.000566 s +[racon::Polisher::initialize] loaded sequences 0.040362 s +[racon::Polisher::initialize] loaded overlaps 0.000339 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.038735 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.059989 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.087509 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.107520 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.133455 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.156161 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.212308 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.240093 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.262407 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.282227 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.309399 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.332741 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.358373 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.370590 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.386684 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.421763 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.435070 s [racon::Polisher::initialize] aligning overlaps [==================> ] 0.455048 s [racon::Polisher::initialize] aligning overlaps [===================>] 0.490919 s [racon::Polisher::initialize] aligning overlaps [====================] 0.522480 s +[racon::Polisher::initialize] transformed data into windows 0.021612 s +[racon::Polisher::polish] generating consensus [=> ] 0.441309 s [racon::Polisher::polish] generating consensus [==> ] 0.852912 s [racon::Polisher::polish] generating consensus [===> ] 1.185648 s [racon::Polisher::polish] generating consensus [====> ] 1.448218 s [racon::Polisher::polish] generating consensus [=====> ] 1.582998 s [racon::Polisher::polish] generating consensus [======> ] 1.746821 s [racon::Polisher::polish] generating consensus [=======> ] 1.893050 s [racon::Polisher::polish] generating consensus [========> ] 2.074662 s [racon::Polisher::polish] generating consensus [=========> ] 2.347789 s [racon::Polisher::polish] generating consensus [==========> ] 2.656391 s [racon::Polisher::polish] generating consensus [===========> ] 3.140528 s [racon::Polisher::polish] generating consensus [============> ] 3.763048 s [racon::Polisher::polish] generating consensus [=============> ] 4.583684 s [racon::Polisher::polish] generating consensus [==============> ] 5.563971 s [racon::Polisher::polish] generating consensus [===============> ] 6.138970 s [racon::Polisher::polish] generating consensus [================> ] 6.556050 s [racon::Polisher::polish] generating consensus [=================> ] 7.061694 s [racon::Polisher::polish] generating consensus [==================> ] 7.490641 s [racon::Polisher::polish] generating consensus [===================>] 8.074710 s [racon::Polisher::polish] generating consensus [====================] 10.116270 s +[racon::Polisher::] total = 10.740797 s +[ OK ] RaconPolishingTest.ConsensusWithQualitiesEditDistance (10757 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualities -[racon::Polisher::initialize] loaded target sequences 0.060482 s -[racon::Polisher::initialize] loaded sequences 0.063037 s -[racon::Polisher::initialize] loaded overlaps 0.042132 s -[racon::Polisher::initialize] aligning overlaps [=> ] 0.167944 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.237075 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.317058 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.393057 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.501075 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.561056 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.721047 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.793046 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.865053 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.925051 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.989061 s [racon::Polisher::initialize] aligning overlaps [============> ] 1.085046 s [racon::Polisher::initialize] aligning overlaps [=============> ] 1.229050 s [racon::Polisher::initialize] aligning overlaps [==============> ] 1.389049 s [racon::Polisher::initialize] aligning overlaps [===============> ] 1.477083 s [racon::Polisher::initialize] aligning overlaps [================> ] 1.561048 s [racon::Polisher::initialize] aligning overlaps [=================> ] 1.661038 s [racon::Polisher::initialize] aligning overlaps [==================> ] 1.805043 s [racon::Polisher::initialize] aligning overlaps [===================>] 1.805069 s [racon::Polisher::initialize] aligning overlaps [====================] 1.869587 s -[racon::Polisher::initialize] transformed data into windows 0.160662 s -[racon::Polisher::polish] generating consensus [=> ] 0.786832 s [racon::Polisher::polish] generating consensus [==> ] 1.377069 s [racon::Polisher::polish] generating consensus [===> ] 1.993736 s [racon::Polisher::polish] generating consensus [====> ] 1.993935 s [racon::Polisher::polish] generating consensus [=====> ] 2.326329 s [racon::Polisher::polish] generating consensus [======> ] 2.520058 s [racon::Polisher::polish] generating consensus [=======> ] 2.816374 s [racon::Polisher::polish] generating consensus [========> ] 2.878738 s [racon::Polisher::polish] generating consensus [=========> ] 3.558923 s [racon::Polisher::polish] generating consensus [==========> ] 3.874922 s [racon::Polisher::polish] generating consensus [===========> ] 4.203057 s [racon::Polisher::polish] generating consensus [============> ] 4.335006 s [racon::Polisher::polish] generating consensus [=============> ] 4.718979 s [racon::Polisher::polish] generating consensus [==============> ] 4.719807 s [racon::Polisher::polish] generating consensus [===============> ] 5.294789 s [racon::Polisher::polish] generating consensus [================> ] 5.294997 s [racon::Polisher::polish] generating consensus [=================> ] 6.878702 s [racon::Polisher::polish] generating consensus [==================> ] 7.241725 s [racon::Polisher::polish] generating consensus [===================>] 7.394553 s [racon::Polisher::polish] generating consensus [====================] 7.428708 s -[racon::Polisher::] total = 9.626792 s -[ OK ] RaconPolishingTest.FragmentCorrectionWithQualities (9654 ms) +[racon::Polisher::initialize] loaded target sequences 0.054473 s +[racon::Polisher::initialize] loaded sequences 0.056251 s +[racon::Polisher::initialize] loaded overlaps 0.016229 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.124010 s [racon::Polisher::initialize] aligning overlaps [==> ] 0.268072 s [racon::Polisher::initialize] aligning overlaps [===> ] 0.303606 s [racon::Polisher::initialize] aligning overlaps [====> ] 0.339585 s [racon::Polisher::initialize] aligning overlaps [=====> ] 0.371580 s [racon::Polisher::initialize] aligning overlaps [======> ] 0.435584 s [racon::Polisher::initialize] aligning overlaps [=======> ] 0.459603 s [racon::Polisher::initialize] aligning overlaps [========> ] 0.491583 s [racon::Polisher::initialize] aligning overlaps [=========> ] 0.543582 s [racon::Polisher::initialize] aligning overlaps [==========> ] 0.615965 s [racon::Polisher::initialize] aligning overlaps [===========> ] 0.665237 s [racon::Polisher::initialize] aligning overlaps [============> ] 0.699998 s [racon::Polisher::initialize] aligning overlaps [=============> ] 0.751979 s [racon::Polisher::initialize] aligning overlaps [==============> ] 0.816063 s [racon::Polisher::initialize] aligning overlaps [===============> ] 0.860039 s [racon::Polisher::initialize] aligning overlaps [================> ] 0.916060 s [racon::Polisher::initialize] aligning overlaps [=================> ] 0.968034 s [racon::Polisher::initialize] aligning overlaps [==================> ] 1.012126 s [racon::Polisher::initialize] aligning overlaps [===================>] 1.032050 s [racon::Polisher::initialize] aligning overlaps [====================] 1.041147 s +[racon::Polisher::initialize] transformed data into windows 0.027608 s +[racon::Polisher::polish] generating consensus [=> ] 0.410714 s [racon::Polisher::polish] generating consensus [==> ] 0.807382 s [racon::Polisher::polish] generating consensus [===> ] 1.072822 s [racon::Polisher::polish] generating consensus [====> ] 1.073545 s [racon::Polisher::polish] generating consensus [=====> ] 1.308492 s [racon::Polisher::polish] generating consensus [======> ] 1.435959 s [racon::Polisher::polish] generating consensus [=======> ] 1.645863 s [racon::Polisher::polish] generating consensus [========> ] 1.689663 s [racon::Polisher::polish] generating consensus [=========> ] 2.123226 s [racon::Polisher::polish] generating consensus [==========> ] 2.294809 s [racon::Polisher::polish] generating consensus [===========> ] 2.434888 s [racon::Polisher::polish] generating consensus [============> ] 2.485204 s [racon::Polisher::polish] generating consensus [=============> ] 2.656508 s [racon::Polisher::polish] generating consensus [==============> ] 2.657253 s [racon::Polisher::polish] generating consensus [===============> ] 3.046568 s [racon::Polisher::polish] generating consensus [================> ] 3.047227 s [racon::Polisher::polish] generating consensus [=================> ] 3.823748 s [racon::Polisher::polish] generating consensus [==================> ] 4.084864 s [racon::Polisher::polish] generating consensus [===================>] 4.325994 s [racon::Polisher::polish] generating consensus [====================] 4.392232 s +[racon::Polisher::] total = 5.589947 s +[ OK ] RaconPolishingTest.FragmentCorrectionWithQualities (5605 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull -[racon::Polisher::initialize] loaded target sequences 0.064108 s -[racon::Polisher::initialize] loaded sequences 0.063423 s -[racon::Polisher::initialize] loaded overlaps 0.017280 s -[racon::Polisher::initialize] aligning overlaps [=> ] 2.064324 s [racon::Polisher::initialize] aligning overlaps [==> ] 3.360335 s [racon::Polisher::initialize] aligning overlaps [===> ] 4.500743 s [racon::Polisher::initialize] aligning overlaps [====> ] 5.936784 s [racon::Polisher::initialize] aligning overlaps [=====> ] 7.104771 s [racon::Polisher::initialize] aligning overlaps [======> ] 7.872373 s [racon::Polisher::initialize] aligning overlaps [=======> ] 9.012745 s [racon::Polisher::initialize] aligning overlaps [========> ] 10.500735 s [racon::Polisher::initialize] aligning overlaps [=========> ] 11.732633 s [racon::Polisher::initialize] aligning overlaps [==========> ] 12.993067 s [racon::Polisher::initialize] aligning overlaps [===========> ] 14.012348 s [racon::Polisher::initialize] aligning overlaps [============> ] 15.604698 s [racon::Polisher::initialize] aligning overlaps [=============> ] 17.112708 s [racon::Polisher::initialize] aligning overlaps [==============> ] 18.564321 s [racon::Polisher::initialize] aligning overlaps [===============> ] 20.076329 s [racon::Polisher::initialize] aligning overlaps [================> ] 21.380466 s [racon::Polisher::initialize] aligning overlaps [=================> ] 22.472461 s [racon::Polisher::initialize] aligning overlaps [==================> ] 23.704780 s [racon::Polisher::initialize] aligning overlaps [===================>] 25.408325 s [racon::Polisher::initialize] aligning overlaps [====================] 26.049635 s -[racon::Polisher::initialize] transformed data into windows 2.213458 s -[racon::Polisher::polish] generating consensus [=> ] 27.618121 s [racon::Polisher::polish] generating consensus [==> ] 44.438503 s [racon::Polisher::polish] generating consensus [===> ] 61.530185 s [racon::Polisher::polish] generating consensus [====> ] 77.684179 s [racon::Polisher::polish] generating consensus [=====> ] 97.650110 s [racon::Polisher::polish] generating consensus [======> ] 116.138086 s [racon::Polisher::polish] generating consensus [=======> ] 138.594529 s [racon::Polisher::polish] generating consensus [========> ] 152.354251 s [racon::Polisher::polish] generating consensus [=========> ] 170.430123 s [racon::Polisher::polish] generating consensus [==========> ] 194.722081 s [racon::Polisher::polish] generating consensus [===========> ] 212.202457 s [racon::Polisher::polish] generating consensus [============> ] 234.498138 s [racon::Polisher::polish] generating consensus [=============> ] 253.190107 s [racon::Polisher::polish] generating consensus [==============> ] 275.086090 s [racon::Polisher::polish] generating consensus [===============> ] 297.494491 s [racon::Polisher::polish] generating consensus [================> ] 309.666551 s [racon::Polisher::polish] generating consensus [=================> ] 331.794522 s [racon::Polisher::polish] generating consensus [==================> ] 356.858141 s [racon::Polisher::polish] generating consensus [===================>] 376.998095 s [racon::Polisher::polish] generating consensus [====================] 398.331719 s -[racon::Polisher::] total = 426.745055 s -[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull (426776 ms) +[racon::Polisher::initialize] loaded target sequences 0.040046 s +[racon::Polisher::initialize] loaded sequences 0.040769 s +[racon::Polisher::initialize] loaded overlaps 0.008768 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.883135 s [racon::Polisher::initialize] aligning overlaps [==> ] 1.310112 s [racon::Polisher::initialize] aligning overlaps [===> ] 1.695180 s [racon::Polisher::initialize] aligning overlaps [====> ] 2.238226 s [racon::Polisher::initialize] aligning overlaps [=====> ] 2.620988 s [racon::Polisher::initialize] aligning overlaps [======> ] 2.981082 s [racon::Polisher::initialize] aligning overlaps [=======> ] 3.431332 s [racon::Polisher::initialize] aligning overlaps [========> ] 4.041275 s [racon::Polisher::initialize] aligning overlaps [=========> ] 4.663087 s [racon::Polisher::initialize] aligning overlaps [==========> ] 5.161556 s [racon::Polisher::initialize] aligning overlaps [===========> ] 5.579264 s [racon::Polisher::initialize] aligning overlaps [============> ] 6.199239 s [racon::Polisher::initialize] aligning overlaps [=============> ] 6.880460 s [racon::Polisher::initialize] aligning overlaps [==============> ] 7.454553 s [racon::Polisher::initialize] aligning overlaps [===============> ] 8.146640 s [racon::Polisher::initialize] aligning overlaps [================> ] 8.790801 s [racon::Polisher::initialize] aligning overlaps [=================> ] 9.330873 s [racon::Polisher::initialize] aligning overlaps [==================> ] 10.021795 s [racon::Polisher::initialize] aligning overlaps [===================>] 10.731955 s [racon::Polisher::initialize] aligning overlaps [====================] 11.077790 s +[racon::Polisher::initialize] transformed data into windows 0.655432 s +[racon::Polisher::polish] generating consensus [=> ] 16.614301 s [racon::Polisher::polish] generating consensus [==> ] 31.397829 s [racon::Polisher::polish] generating consensus [===> ] 45.329620 s [racon::Polisher::polish] generating consensus [====> ] 55.717550 s [racon::Polisher::polish] generating consensus [=====> ] 66.526992 s [racon::Polisher::polish] generating consensus [======> ] 79.468677 s [racon::Polisher::polish] generating consensus [=======> ] 93.069599 s [racon::Polisher::polish] generating consensus [========> ] 102.694599 s [racon::Polisher::polish] generating consensus [=========> ] 114.844538 s [racon::Polisher::polish] generating consensus [==========> ] 133.342518 s [racon::Polisher::polish] generating consensus [===========> ] 145.871562 s [racon::Polisher::polish] generating consensus [============> ] 159.430929 s [racon::Polisher::polish] generating consensus [=============> ] 171.282951 s [racon::Polisher::polish] generating consensus [==============> ] 183.702361 s [racon::Polisher::polish] generating consensus [===============> ] 197.661052 s [racon::Polisher::polish] generating consensus [================> ] 205.120388 s [racon::Polisher::polish] generating consensus [=================> ] 219.943392 s [racon::Polisher::polish] generating consensus [==================> ] 233.906964 s [racon::Polisher::polish] generating consensus [===================>] 247.259725 s [racon::Polisher::polish] generating consensus [====================] 257.424083 s +[racon::Polisher::] total = 269.251768 s +[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFull (269263 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull -[racon::Polisher::initialize] loaded target sequences 0.029005 s -[racon::Polisher::initialize] loaded sequences 0.029329 s -[racon::Polisher::initialize] loaded overlaps 0.017689 s -[racon::Polisher::initialize] aligning overlaps [=> ] 2.228909 s [racon::Polisher::initialize] aligning overlaps [==> ] 3.546867 s [racon::Polisher::initialize] aligning overlaps [===> ] 4.563566 s [racon::Polisher::initialize] aligning overlaps [====> ] 6.211436 s [racon::Polisher::initialize] aligning overlaps [=====> ] 7.591866 s [racon::Polisher::initialize] aligning overlaps [======> ] 8.526496 s [racon::Polisher::initialize] aligning overlaps [=======> ] 10.035429 s [racon::Polisher::initialize] aligning overlaps [========> ] 11.662821 s [racon::Polisher::initialize] aligning overlaps [=========> ] 13.395441 s [racon::Polisher::initialize] aligning overlaps [==========> ] 15.231423 s [racon::Polisher::initialize] aligning overlaps [===========> ] 16.207410 s [racon::Polisher::initialize] aligning overlaps [============> ] 17.863400 s [racon::Polisher::initialize] aligning overlaps [=============> ] 19.663832 s [racon::Polisher::initialize] aligning overlaps [==============> ] 21.234604 s [racon::Polisher::initialize] aligning overlaps [===============> ] 22.743714 s [racon::Polisher::initialize] aligning overlaps [================> ] 24.123715 s [racon::Polisher::initialize] aligning overlaps [=================> ] 26.003022 s [racon::Polisher::initialize] aligning overlaps [==================> ] 28.002123 s [racon::Polisher::initialize] aligning overlaps [===================>] 29.751407 s [racon::Polisher::initialize] aligning overlaps [====================] 31.089236 s -[racon::Polisher::initialize] transformed data into windows 0.025330 s -[racon::Polisher::polish] generating consensus [=> ] 39.826906 s [racon::Polisher::polish] generating consensus [==> ] 65.099412 s [racon::Polisher::polish] generating consensus [===> ] 96.443106 s [racon::Polisher::polish] generating consensus [====> ] 116.266940 s [racon::Polisher::polish] generating consensus [=====> ] 137.349464 s [racon::Polisher::polish] generating consensus [======> ] 162.017803 s [racon::Polisher::polish] generating consensus [=======> ] 189.270682 s [racon::Polisher::polish] generating consensus [========> ] 208.453693 s [racon::Polisher::polish] generating consensus [=========> ] 233.539329 s [racon::Polisher::polish] generating consensus [==========> ] 261.664480 s [racon::Polisher::polish] generating consensus [===========> ] 287.142630 s [racon::Polisher::polish] generating consensus [============> ] 315.373766 s [racon::Polisher::polish] generating consensus [=============> ] 339.971025 s [racon::Polisher::polish] generating consensus [==============> ] 371.607006 s [racon::Polisher::polish] generating consensus [===============> ] 405.655182 s [racon::Polisher::polish] generating consensus [================> ] 420.303134 s [racon::Polisher::polish] generating consensus [=================> ] 455.214948 s [racon::Polisher::polish] generating consensus [==================> ] 485.286625 s [racon::Polisher::polish] generating consensus [===================>] 511.506602 s [racon::Polisher::polish] generating consensus [====================] 523.443224 s -[racon::Polisher::] total = 554.638072 s -[ OK ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull (554667 ms) +[racon::Polisher::initialize] loaded target sequences 0.025870 s +[racon::Polisher::initialize] loaded sequences 0.018601 s +[racon::Polisher::initialize] loaded overlaps 0.008825 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.646965 s [racon::Polisher::initialize] aligning overlaps [==> ] 1.067958 s [racon::Polisher::initialize] aligning overlaps [===> ] 1.447485 s [racon::Polisher::initialize] aligning overlaps [====> ] 2.020158 s [racon::Polisher::initialize] aligning overlaps [=====> ] 2.514429 s [racon::Polisher::initialize] aligning overlaps [======> ] 2.849876 s [racon::Polisher::initialize] aligning overlaps [=======> ] 3.318753 s [racon::Polisher::initialize] aligning overlaps [========> ] 3.930831 s [racon::Polisher::initialize] aligning overlaps [=========> ] 4.480396 s [racon::Polisher::initialize] aligning overlaps [==========> ] 5.038866 s [racon::Polisher::initialize] aligning overlaps [===========> ] 5.459618 s [racon::Polisher::initialize] aligning overlaps [============> ] 6.069782 s [racon::Polisher::initialize] aligning overlaps [=============> ] 6.689812 s [racon::Polisher::initialize] aligning overlaps [==============> ] 7.236369 s [racon::Polisher::initialize] aligning overlaps [===============> ] 7.933481 s [racon::Polisher::initialize] aligning overlaps [================> ] 8.574662 s [racon::Polisher::initialize] aligning overlaps [=================> ] 9.122563 s [racon::Polisher::initialize] aligning overlaps [==================> ] 9.804437 s [racon::Polisher::initialize] aligning overlaps [===================>] 10.519006 s [racon::Polisher::initialize] aligning overlaps [====================] 10.985678 s +[racon::Polisher::initialize] transformed data into windows 0.014301 s +[racon::Polisher::polish] generating consensus [=> ] 21.875290 s [racon::Polisher::polish] generating consensus [==> ] 38.812654 s [racon::Polisher::polish] generating consensus [===> ] 55.899426 s [racon::Polisher::polish] generating consensus [====> ] 68.716596 s [racon::Polisher::polish] generating consensus [=====> ] 84.069538 s [racon::Polisher::polish] generating consensus [======> ] 104.141782 s [racon::Polisher::polish] generating consensus [=======> ] 123.249593 s [racon::Polisher::polish] generating consensus [========> ] 137.149677 s [racon::Polisher::polish] generating consensus [=========> ] 154.606810 s [racon::Polisher::polish] generating consensus [==========> ] 174.954503 s [racon::Polisher::polish] generating consensus [===========> ] 193.280911 s [racon::Polisher::polish] generating consensus [============> ] 211.851421 s [racon::Polisher::polish] generating consensus [=============> ] 229.087074 s [racon::Polisher::polish] generating consensus [==============> ] 246.662478 s [racon::Polisher::polish] generating consensus [===============> ] 264.275820 s [racon::Polisher::polish] generating consensus [================> ] 274.061735 s [racon::Polisher::polish] generating consensus [=================> ] 296.566085 s [racon::Polisher::polish] generating consensus [==================> ] 317.440681 s [racon::Polisher::polish] generating consensus [===================>] 335.200284 s [racon::Polisher::polish] generating consensus [====================] 351.449943 s +[racon::Polisher::] total = 362.505712 s +[ OK ] RaconPolishingTest.FragmentCorrectionWithoutQualitiesFull (362526 ms) [ RUN ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap -[racon::Polisher::initialize] loaded target sequences 0.057365 s -[racon::Polisher::initialize] loaded sequences 0.056278 s -[racon::Polisher::initialize] loaded overlaps 0.024263 s -[racon::Polisher::initialize] aligning overlaps [=> ] 1.189289 s [racon::Polisher::initialize] aligning overlaps [==> ] 1.970594 s [racon::Polisher::initialize] aligning overlaps [===> ] 2.661068 s [racon::Polisher::initialize] aligning overlaps [====> ] 3.640914 s [racon::Polisher::initialize] aligning overlaps [=====> ] 4.485918 s [racon::Polisher::initialize] aligning overlaps [======> ] 5.052563 s [racon::Polisher::initialize] aligning overlaps [=======> ] 5.867443 s [racon::Polisher::initialize] aligning overlaps [========> ] 6.927867 s [racon::Polisher::initialize] aligning overlaps [=========> ] 7.895263 s [racon::Polisher::initialize] aligning overlaps [==========> ] 8.791511 s [racon::Polisher::initialize] aligning overlaps [===========> ] 9.520092 s [racon::Polisher::initialize] aligning overlaps [============> ] 10.765507 s [racon::Polisher::initialize] aligning overlaps [=============> ] 12.004325 s [racon::Polisher::initialize] aligning overlaps [==============> ] 13.102405 s [racon::Polisher::initialize] aligning overlaps [===============> ] 14.281362 s [racon::Polisher::initialize] aligning overlaps [================> ] 15.347626 s [racon::Polisher::initialize] aligning overlaps [=================> ] 16.655707 s [racon::Polisher::initialize] aligning overlaps [==================> ] 17.796015 s [racon::Polisher::initialize] aligning overlaps [===================>] 18.786022 s [racon::Polisher::initialize] aligning overlaps [====================] 19.043787 s -[racon::Polisher::initialize] transformed data into windows 1.948642 s -[racon::Polisher::polish] generating consensus [=> ] 20.279446 s [racon::Polisher::polish] generating consensus [==> ] 34.650748 s [racon::Polisher::polish] generating consensus [===> ] 50.930155 s [racon::Polisher::polish] generating consensus [====> ] 64.246260 s [racon::Polisher::polish] generating consensus [=====> ] 78.529753 s [racon::Polisher::polish] generating consensus [======> ] 95.451892 s [racon::Polisher::polish] generating consensus [=======> ] 112.813918 s [racon::Polisher::polish] generating consensus [========> ] 125.372074 s [racon::Polisher::polish] generating consensus [=========> ] 141.339621 s [racon::Polisher::polish] generating consensus [==========> ] 160.495335 s [racon::Polisher::polish] generating consensus [===========> ] 176.195365 s [racon::Polisher::polish] generating consensus [============> ] 194.210976 s [racon::Polisher::polish] generating consensus [=============> ] 209.623189 s [racon::Polisher::polish] generating consensus [==============> ] 226.210844 s [racon::Polisher::polish] generating consensus [===============> ] 244.536178 s [racon::Polisher::polish] generating consensus [================> ] 255.045248 s [racon::Polisher::polish] generating consensus [=================> ] 277.013728 s [racon::Polisher::polish] generating consensus [==================> ] 303.981879 s [racon::Polisher::polish] generating consensus [===================>] 327.065229 s [racon::Polisher::polish] generating consensus [====================] 340.430017 s -[racon::Polisher::] total = 361.564577 s -[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap (361591 ms) -[----------] 10 tests from RaconPolishingTest (1470785 ms total) +[racon::Polisher::initialize] loaded target sequences 0.041286 s +[racon::Polisher::initialize] loaded sequences 0.040993 s +[racon::Polisher::initialize] loaded overlaps 0.008876 s +[racon::Polisher::initialize] aligning overlaps [=> ] 0.642570 s [racon::Polisher::initialize] aligning overlaps [==> ] 1.060264 s [racon::Polisher::initialize] aligning overlaps [===> ] 1.447749 s [racon::Polisher::initialize] aligning overlaps [====> ] 2.019742 s [racon::Polisher::initialize] aligning overlaps [=====> ] 2.509022 s [racon::Polisher::initialize] aligning overlaps [======> ] 2.843098 s [racon::Polisher::initialize] aligning overlaps [=======> ] 3.311076 s [racon::Polisher::initialize] aligning overlaps [========> ] 3.921360 s [racon::Polisher::initialize] aligning overlaps [=========> ] 4.470483 s [racon::Polisher::initialize] aligning overlaps [==========> ] 5.026513 s [racon::Polisher::initialize] aligning overlaps [===========> ] 5.446706 s [racon::Polisher::initialize] aligning overlaps [============> ] 6.059936 s [racon::Polisher::initialize] aligning overlaps [=============> ] 6.679635 s [racon::Polisher::initialize] aligning overlaps [==============> ] 7.188383 s [racon::Polisher::initialize] aligning overlaps [===============> ] 7.896877 s [racon::Polisher::initialize] aligning overlaps [================> ] 8.545321 s [racon::Polisher::initialize] aligning overlaps [=================> ] 9.121335 s [racon::Polisher::initialize] aligning overlaps [==================> ] 9.771398 s [racon::Polisher::initialize] aligning overlaps [===================>] 10.436334 s [racon::Polisher::initialize] aligning overlaps [====================] 10.967872 s +[racon::Polisher::initialize] transformed data into windows 0.590362 s +[racon::Polisher::polish] generating consensus [=> ] 15.849244 s [racon::Polisher::polish] generating consensus [==> ] 27.149706 s [racon::Polisher::polish] generating consensus [===> ] 39.520699 s [racon::Polisher::polish] generating consensus [====> ] 50.013428 s [racon::Polisher::polish] generating consensus [=====> ] 60.888287 s [racon::Polisher::polish] generating consensus [======> ] 75.516062 s [racon::Polisher::polish] generating consensus [=======> ] 96.909343 s [racon::Polisher::polish] generating consensus [========> ] 108.350137 s [racon::Polisher::polish] generating consensus [=========> ] 121.695886 s [racon::Polisher::polish] generating consensus [==========> ] 141.018196 s [racon::Polisher::polish] generating consensus [===========> ] 158.576084 s [racon::Polisher::polish] generating consensus [============> ] 179.097922 s [racon::Polisher::polish] generating consensus [=============> ] 194.942640 s [racon::Polisher::polish] generating consensus [==============> ] 209.428998 s [racon::Polisher::polish] generating consensus [===============> ] 224.116324 s [racon::Polisher::polish] generating consensus [================> ] 232.496420 s [racon::Polisher::polish] generating consensus [=================> ] 247.632646 s [racon::Polisher::polish] generating consensus [==================> ] 262.648366 s [racon::Polisher::polish] generating consensus [===================>] 276.324354 s [racon::Polisher::polish] generating consensus [====================] 290.691894 s +[racon::Polisher::] total = 302.949464 s +[ OK ] RaconPolishingTest.FragmentCorrectionWithQualitiesFullMhap (302976 ms) +[----------] 10 tests from RaconPolishingTest (1041859 ms total) [----------] Global test environment tear-down -[==========] 15 tests from 2 test suites ran. (1470862 ms total) +[==========] 15 tests from 2 test suites ran. (1041868 ms total) [ PASSED ] 15 tests. make[1]: Leaving directory '/build/reproducible-path/racon-1.5.0' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=cmake dh_prep -O--buildsystem=cmake dh_auto_install --destdir=debian/racon/ -O--buildsystem=cmake - cd obj-i686-linux-gnu && make -j8 install DESTDIR=/build/reproducible-path/racon-1.5.0/debian/racon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j21 install DESTDIR=/build/reproducible-path/racon-1.5.0/debian/racon AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/racon-1.5.0 -B/build/reproducible-path/racon-1.5.0/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -731,12 +767,14 @@ 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/33246/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/33246/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/60059 and its subdirectories -I: Current time: Mon Mar 25 14:56:51 -12 2024 -I: pbuilder-time-stamp: 1711421811 +I: removing directory /srv/workspace/pbuilder/33246 and its subdirectories +I: Current time: Mon Apr 28 23:38:58 +14 2025 +I: pbuilder-time-stamp: 1745833138