Diff of the two buildlogs: -- --- b1/build.log 2024-05-31 08:30:49.858760657 +0000 +++ b2/build.log 2024-05-31 08:34:09.694243663 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Thu Jul 3 02:50:00 -12 2025 -I: pbuilder-time-stamp: 1751554200 +I: Current time: Fri May 31 22:30:52 +14 2024 +I: pbuilder-time-stamp: 1717144252 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,51 +26,83 @@ dpkg-source: info: unpacking diamond-aligner_2.1.9-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/982005/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2386646/tmp/hooks/D01_modify_environment starting +debug: Running on infom01-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 May 31 08:31 /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/2386646/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2386646/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='amd64' - DEBIAN_FRONTEND='noninteractive' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="x86_64-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=amd64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='amd64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='0b2e516ef70145e8bdef1fd790cb74da' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='982005' - PS1='# ' - PS2='> ' + INVOCATION_ID=f935376b6c774ce5a449a65b1f03cb6e + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=2386646 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.UvCWFvpp/pbuilderrc_zYvc --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.UvCWFvpp/b1 --logfile b1/build.log diamond-aligner_2.1.9-1.dsc' - SUDO_GID='109' - SUDO_UID='104' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' + 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.UvCWFvpp/pbuilderrc_3JZf --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.UvCWFvpp/b2 --logfile b2/build.log diamond-aligner_2.1.9-1.dsc' + SUDO_GID=109 + SUDO_UID=104 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' I: uname -a - Linux infom02-amd64 6.7.12+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.7.12-1~bpo12+1 (2024-05-06) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-21-cloud-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Jun 28 17:46 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/982005/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 May 26 11:24 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2386646/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -166,7 +198,7 @@ Get: 52 http://deb.debian.org/debian trixie/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian trixie/main amd64 debhelper all 13.15.3 [901 kB] Get: 54 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB] -Fetched 36.6 MB in 1s (39.1 MB/s) +Fetched 36.6 MB in 0s (97.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libproc2-0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19699 files and directories currently installed.) @@ -397,7 +429,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/diamond-aligner-2.1.9/ && 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 > ../diamond-aligner_2.1.9-1_source.changes +I: user script /srv/workspace/pbuilder/2386646/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/2386646/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/diamond-aligner-2.1.9/ && 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 > ../diamond-aligner_2.1.9-1_source.changes dpkg-buildpackage: info: source package diamond-aligner dpkg-buildpackage: info: source version 2.1.9-1 dpkg-buildpackage: info: source distribution unstable @@ -453,7 +489,7 @@ -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE --- Configuring done (1.9s) +-- Configuring done (1.4s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -482,78 +518,78 @@ make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' cd /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu/CMakeFiles/arch_generic.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' -cd /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu/CMakeFiles/arch_sse4_1.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' cd /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu/CMakeFiles/arch_avx2.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9 /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu/CMakeFiles/arch_sse4_1.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' -make -f CMakeFiles/arch_avx2.dir/build.make CMakeFiles/arch_avx2.dir/build +make -f CMakeFiles/arch_generic.dir/build.make CMakeFiles/arch_generic.dir/build +make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' -make -f CMakeFiles/arch_generic.dir/build.make CMakeFiles/arch_generic.dir/build make -f CMakeFiles/arch_sse4_1.dir/build.make CMakeFiles/arch_sse4_1.dir/build make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' +make -f CMakeFiles/arch_avx2.dir/build.make CMakeFiles/arch_avx2.dir/build make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' -make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' -[ 1%] Building CXX object CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o -[ 1%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -[ 1%] Building CXX object CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o -[ 1%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o [ 1%] Building CXX object CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -[ 2%] Building CXX object CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o -[ 3%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/swipe/swipe_wrapper.cpp.o -[ 4%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/scan_diags.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o -MF CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/search/stage1_2.cpp -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_SSE4_1 -DARCH_ID=1 -mssse3 -mpopcnt -msse4.1 -DEigen=Eigen_SSE4_1 -MD -MT CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -MF CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o.d -o CMakeFiles/arch_sse4_1.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/banded_3frame_swipe.cpp -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o -MF CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/tools/benchmark.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/tools/benchmark.cpp -[ 5%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/search/stage1_2.cpp.o +[ 1%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_wrapper.cpp.o +[ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/scan_diags.cpp.o +[ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o +[ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.cpp.o +[ 3%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -MF CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o.d -o CMakeFiles/arch_generic.dir/src/tools/benchmark.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/tools/benchmark.cpp +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra 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-D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o -MF CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/search/stage1_2.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/search/stage1_2.cpp +[ 11%] Building CXX object CMakeFiles/arch_sse4_1.dir/src/dp/score_profile.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/masking/tantan.cpp.o -MF CMakeFiles/arch_avx2.dir/src/masking/tantan.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/masking/tantan.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/masking/tantan.cpp +[ 13%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/scan_diags.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 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-DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/ungapped_simd.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/ungapped_simd.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/ungapped_simd.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/ungapped_simd.cpp +[ 14%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/pfscan/pfscan.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/pfscan/pfscan.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/pfscan/pfscan.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/pfscan/pfscan.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/pfscan/pfscan.cpp +[ 14%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/swipe/anchored_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/anchored_wrapper.cpp +[ 15%] Building CXX object CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -DDISPATCH_ARCH=ARCH_AVX2 -DARCH_ID=2 -mssse3 -mpopcnt -msse4.1 -msse4.2 -mavx -mavx2 -DEigen=Eigen_AVX2 -MD -MT CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o -MF CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o.d -o CMakeFiles/arch_avx2.dir/src/dp/score_profile.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/score_profile.cpp In file included from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/../../basic/../util/string/string.h:4, from /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/../../basic/../util/text_buffer.h:31, @@ -598,11 +634,11 @@ cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' [ 15%] Built target arch_generic -make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' -[ 15%] Built target arch_avx2 At global scope: cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics make[3]: Leaving directory 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warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -800,19 +840,12 @@ /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -[ 60%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstat.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG 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CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstatmatrix.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstatmatrix.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstatmatrix.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_localmaxstatmatrix.cpp [ 61%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstatutil.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstatutil.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstatutil.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/njn_localmaxstatutil.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_localmaxstatutil.cpp -cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics [ 61%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/njn_random.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter 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option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics In file included from /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_dynprogproblim.hpp:39, from /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_localmaxstatutil.cpp:39: /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_dynprogprob.hpp:110:37: warning: ‘virtual Njn::DynProgProb& Njn::DynProgProb::operator=(const Njn::DynProgProb&)’ was hidden [-Woverloaded-virtual=] @@ -855,16 +894,13 @@ /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_dynprogproblim.hpp:101:29: note: by ‘Njn::DynProgProbLim::copy’ 101 | virtual inline void copy ( | ^~~~ -cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics -[ 64%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/sls_alp_regression.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND 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CMakeFiles/diamond.dir/src/align/global_ranking/global_ranking.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/align/global_ranking/global_ranking.cpp.o -MF CMakeFiles/diamond.dir/src/align/global_ranking/global_ranking.cpp.o.d -o CMakeFiles/diamond.dir/src/align/global_ranking/global_ranking.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/align/global_ranking/global_ranking.cpp [ 66%] Building CXX object CMakeFiles/diamond.dir/src/align/global_ranking/extend.cpp.o @@ -882,8 +918,8 @@ [ 69%] Building CXX object CMakeFiles/diamond.dir/src/stats/matrices/blosum50.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/matrices/blosum50.cpp.o -MF CMakeFiles/diamond.dir/src/stats/matrices/blosum50.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/matrices/blosum50.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/stats/matrices/blosum50.cpp [ 70%] Building CXX object CMakeFiles/diamond.dir/src/stats/matrices/blosum62.cpp.o -[ 70%] Building CXX object CMakeFiles/diamond.dir/src/stats/matrices/blosum80.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/matrices/blosum62.cpp.o -MF CMakeFiles/diamond.dir/src/stats/matrices/blosum62.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/matrices/blosum62.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/stats/matrices/blosum62.cpp +[ 70%] Building CXX object CMakeFiles/diamond.dir/src/stats/matrices/blosum80.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/matrices/blosum80.cpp.o -MF CMakeFiles/diamond.dir/src/stats/matrices/blosum80.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/matrices/blosum80.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/stats/matrices/blosum80.cpp [ 71%] Building CXX object CMakeFiles/diamond.dir/src/stats/matrices/blosum90.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/matrices/blosum90.cpp.o -MF CMakeFiles/diamond.dir/src/stats/matrices/blosum90.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/matrices/blosum90.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/stats/matrices/blosum90.cpp @@ -892,8 +928,8 @@ [ 72%] Building CXX object CMakeFiles/diamond.dir/src/stats/matrices/pam30.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/matrices/pam30.cpp.o -MF CMakeFiles/diamond.dir/src/stats/matrices/pam30.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/matrices/pam30.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/stats/matrices/pam30.cpp [ 72%] Building CXX object CMakeFiles/diamond.dir/src/stats/matrices/pam70.cpp.o -[ 73%] Building CXX object CMakeFiles/diamond.dir/src/stats/stats.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/matrices/pam70.cpp.o -MF CMakeFiles/diamond.dir/src/stats/matrices/pam70.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/matrices/pam70.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/stats/matrices/pam70.cpp +[ 73%] Building CXX object CMakeFiles/diamond.dir/src/stats/stats.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/stats.cpp.o -MF CMakeFiles/diamond.dir/src/stats/stats.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/stats.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/stats/stats.cpp [ 73%] Building CXX object CMakeFiles/diamond.dir/src/stats/cbs.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_AVX2 -DWITH_SSE4_1 -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.9/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.9=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -fuse-ld=gold -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -Wno-implicit-fallthrough -Wreturn-type -Wno-unused -Wno-unused-parameter -Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++17 -MD -MT CMakeFiles/diamond.dir/src/stats/cbs.cpp.o -MF CMakeFiles/diamond.dir/src/stats/cbs.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/cbs.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/stats/cbs.cpp @@ -1014,17 +1050,17 @@ make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9' -cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games sh diamond-calls -+ mktemp -d -+ TESTDIR=/tmp/tmp.P8oDZbS2vc -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.P8oDZbS2vc/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.9/obj-x86_64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path sh diamond-calls +++ mktemp -d ++ TESTDIR=/tmp/tmp.E9mgkFlIle ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.E9mgkFlIle/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -1032,13 +1068,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.007s] +Masking queries... [0.005s] Algorithm: Double-indexed -Building query histograms... [0.011s] +Building query histograms... [0.01s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.004s] -Initializing temporary storage... [0.005s] +Initializing temporary storage... [0s] Building reference histograms... [0.01s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -1046,14 +1082,14 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.002s] @@ -1071,7 +1107,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1085,14 +1121,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1113,7 +1149,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1133,14 +1169,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1225,7 +1261,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1233,7 +1269,7 @@ Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -1252,8 +1288,8 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1308,7 +1344,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1386,14 +1422,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1414,7 +1450,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1469,7 +1505,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1491,12 +1527,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.01s] +Computing alignments... Loading trace points... [0.003s] Sorting trace points... [0s] -Computing alignments... [0.076s] +Computing alignments... [0.077s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.087s] + [0.082s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -1506,17 +1542,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.706s +Total time = 0.724s Reported 77 pairwise alignments, 77 HSPs. 72 queries aligned. -+ diamond blastp --threads 1 --db test/E.faa.diamond --query test/C.faa --out /tmp/tmp.P8oDZbS2vc/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/E.faa.diamond --query test/C.faa --out /tmp/tmp.E9mgkFlIle/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -1524,13 +1560,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.01s] +Masking queries... [0.007s] Algorithm: Double-indexed -Building query histograms... [0.011s] +Building query histograms... [0.01s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.004s] -Initializing temporary storage... [0.006s] +Initializing temporary storage... [0.033s] Building reference histograms... [0.011s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -1538,14 +1574,14 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.003s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.003s] @@ -1555,7 +1591,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1576,7 +1612,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1605,7 +1641,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1632,8 +1668,8 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1648,12 +1684,12 @@ Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1682,20 +1718,20 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1704,7 +1740,7 @@ Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -1716,7 +1752,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1731,7 +1767,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1745,7 +1781,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1758,7 +1794,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1807,7 +1843,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1818,24 +1854,24 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1856,8 +1892,8 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1905,15 +1941,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1940,7 +1976,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1954,14 +1990,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1976,19 +2012,19 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.007s] +Computing alignments... Loading trace points... [0.016s] Sorting trace points... [0s] -Computing alignments... [0.015s] +Computing alignments... [0.013s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.023s] + [0.031s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -1998,17 +2034,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.666s +Total time = 0.722s Reported 41 pairwise alignments, 41 HSPs. 15 queries aligned. -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/L.faa --out /tmp/tmp.P8oDZbS2vc/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/L.faa --out /tmp/tmp.E9mgkFlIle/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -2016,31 +2052,31 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.008s] +Masking queries... [0.005s] Algorithm: Double-indexed -Building query histograms... [0.006s] +Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.004s] -Initializing temporary storage... [0.004s] -Building reference histograms... [0.014s] +Initializing temporary storage... [0.046s] +Building reference histograms... [0.012s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2117,7 +2153,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2174,7 +2210,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2394,7 +2430,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -2432,7 +2468,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2475,12 +2511,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.011s] +Computing alignments... Loading trace points... [0.006s] Sorting trace points... [0s] -Computing alignments... [0.035s] +Computing alignments... [0.034s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.047s] + [0.043s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -2490,31 +2526,31 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.554s +Total time = 0.636s Reported 64 pairwise alignments, 64 HSPs. 33 queries aligned. -+ diamond blastp --threads 1 --db test/L.faa.diamond --query test/C.faa --out /tmp/tmp.P8oDZbS2vc/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/L.faa.diamond --query test/C.faa --out /tmp/tmp.E9mgkFlIle/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) Block size = 2000000000 Opening the input file... [0s] -Opening the output file... [0s] +Opening the output file... [0.001s] Loading query sequences... [0s] -Masking queries... [0.01s] +Masking queries... [0.006s] Algorithm: Double-indexed Building query histograms... [0.01s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.002s] -Initializing temporary storage... [0.004s] +Initializing temporary storage... [0.006s] Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -2529,7 +2565,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -2589,7 +2625,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2813,7 +2849,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2925,7 +2961,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2946,7 +2982,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2967,12 +3003,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.014s] +Computing alignments... Loading trace points... [0.004s] Sorting trace points... [0s] -Computing alignments... [0.062s] +Computing alignments... [0.065s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.079s] + [0.073s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -2982,17 +3018,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.58s +Total time = 0.632s Reported 133 pairwise alignments, 133 HSPs. 109 queries aligned. -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/M.faa --out /tmp/tmp.P8oDZbS2vc/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/M.faa --out /tmp/tmp.E9mgkFlIle/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -3000,31 +3036,31 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.009s] +Masking queries... [0.006s] Algorithm: Double-indexed -Building query histograms... [0.006s] +Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.004s] -Initializing temporary storage... [0.007s] +Initializing temporary storage... [0.016s] Building reference histograms... [0.01s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3040,7 +3076,7 @@ Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.001s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -3080,11 +3116,11 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -3122,7 +3158,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3164,7 +3200,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3304,14 +3340,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3459,12 +3495,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.015s] +Computing alignments... Loading trace points... [0.008s] Sorting trace points... [0s] -Computing alignments... [0.032s] +Computing alignments... [0.042s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.049s] + [0.052s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3474,17 +3510,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.569s +Total time = 0.621s Reported 62 pairwise alignments, 62 HSPs. 33 queries aligned. -+ diamond blastp --threads 1 --db test/M.faa.diamond --query test/C.faa --out /tmp/tmp.P8oDZbS2vc/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/M.faa.diamond --query test/C.faa --out /tmp/tmp.E9mgkFlIle/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -3492,13 +3528,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.011s] +Masking queries... [0.006s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.009s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.002s] -Initializing temporary storage... [0.005s] +Initializing temporary storage... [0.035s] Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -3506,14 +3542,14 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -3545,7 +3581,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3685,7 +3721,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3721,7 +3757,7 @@ Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. Building reference seed array... [0.001s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -3769,7 +3805,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3790,7 +3826,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3846,14 +3882,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3863,7 +3899,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. Building reference seed array... [0.001s] @@ -3888,7 +3924,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3902,14 +3938,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3923,7 +3959,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3951,12 +3987,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.016s] +Computing alignments... Loading trace points... [0.011s] Sorting trace points... [0s] -Computing alignments... [0.063s] +Computing alignments... [0.07s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.08s] + [0.083s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3966,17 +4002,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.608s +Total time = 0.743s Reported 131 pairwise alignments, 131 HSPs. 109 queries aligned. -+ diamond blastp --ignore-warnings --threads 1 --db test/C.faa.diamond --query test/C2.faa --out /tmp/tmp.P8oDZbS2vc/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --ignore-warnings --threads 1 --db test/C.faa.diamond --query test/C2.faa --out /tmp/tmp.E9mgkFlIle/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -3984,14 +4020,14 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0s] Algorithm: Double-indexed Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.004s] -Initializing temporary storage... [0.004s] -Building reference histograms... [0.012s] +Initializing temporary storage... [0.001s] +Building reference histograms... [0.01s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -4008,7 +4044,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4096,7 +4132,7 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -4148,7 +4184,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4166,10 +4202,10 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4197,7 +4233,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4443,12 +4479,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.006s] +Computing alignments... Loading trace points... [0.001s] Sorting trace points... [0s] -Computing alignments... [0s] +Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.008s] + [0.004s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4458,17 +4494,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.434s +Total time = 0.448s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/C.faa --out /tmp/tmp.P8oDZbS2vc/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/C.faa --out /tmp/tmp.E9mgkFlIle/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -4476,13 +4512,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.01s] +Masking queries... [0.006s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.009s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] -Initializing temporary storage... [0.005s] +Initializing temporary storage... [0.041s] Building reference histograms... [0s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -4497,7 +4533,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0s] @@ -4616,7 +4652,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0s] @@ -4661,7 +4697,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4893,7 +4929,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4914,14 +4950,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4935,12 +4971,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.006s] +Computing alignments... Loading trace points... [0.003s] Sorting trace points... [0s] Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.008s] + [0.006s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4950,17 +4986,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.44s +Total time = 0.479s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/E.faa.diamond --query test/L.faa --out /tmp/tmp.P8oDZbS2vc/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/E.faa.diamond --query test/L.faa --out /tmp/tmp.E9mgkFlIle/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -4968,13 +5004,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.008s] +Masking queries... [0.005s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.004s] -Initializing temporary storage... [0.004s] +Initializing temporary storage... [0s] Building reference histograms... [0.01s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -4989,14 +5025,14 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -5006,7 +5042,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5020,7 +5056,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5038,10 +5074,10 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5059,10 +5095,10 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5076,28 +5112,28 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5118,7 +5154,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5181,14 +5217,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5213,14 +5249,14 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -5241,21 +5277,21 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -5269,7 +5305,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0.003s] @@ -5293,7 +5329,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5314,7 +5350,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5329,7 +5365,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5349,7 +5385,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5377,15 +5413,15 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5393,7 +5429,7 @@ Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.001s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -5412,7 +5448,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5427,32 +5463,32 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.008s] +Computing alignments... Loading trace points... [0.083s] Sorting trace points... [0s] -Computing alignments... [0.101s] +Computing alignments... [0.103s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.111s] + [0.188s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] Deallocating queries... [0s] Loading query sequences... [0s] Closing the input file... [0s] -Closing the output file... [0s] +Closing the output file... [0.003s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.66s +Total time = 0.787s Reported 489 pairwise alignments, 489 HSPs. 32 queries aligned. -+ diamond blastp --threads 1 --db test/L.faa.diamond --query test/E.faa --out /tmp/tmp.P8oDZbS2vc/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/L.faa.diamond --query test/E.faa --out /tmp/tmp.E9mgkFlIle/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -5460,21 +5496,21 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.006s] +Masking queries... [0.005s] Algorithm: Double-indexed -Building query histograms... [0.011s] +Building query histograms... [0.01s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.002s] -Initializing temporary storage... [0.007s] +Initializing temporary storage... [0s] Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -5484,11 +5520,11 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0.001s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. Building reference seed array... [0.001s] @@ -5498,7 +5534,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5513,7 +5549,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5541,7 +5577,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5569,7 +5605,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5593,11 +5629,11 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5614,7 +5650,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -5625,7 +5661,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5646,7 +5682,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5660,15 +5696,15 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0.001s] Building query seed array... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -5709,7 +5745,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5737,7 +5773,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5782,18 +5818,18 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5807,7 +5843,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5821,7 +5857,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5842,14 +5878,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5877,7 +5913,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5905,7 +5941,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5919,12 +5955,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.009s] +Computing alignments... Loading trace points... [0.003s] Sorting trace points... [0s] -Computing alignments... [0.206s] +Computing alignments... [0.19s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.218s] + [0.197s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5934,17 +5970,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.766s +Total time = 0.763s Reported 1173 pairwise alignments, 1173 HSPs. 72 queries aligned. -+ diamond blastp --threads 1 --db test/E.faa.diamond --query test/M.faa --out /tmp/tmp.P8oDZbS2vc/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/E.faa.diamond --query test/M.faa --out /tmp/tmp.E9mgkFlIle/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -5952,25 +5988,25 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.008s] +Masking queries... [0.005s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] -Initializing temporary storage... [0.004s] -Building reference histograms... [0.012s] +Masking reference... [0.003s] +Initializing temporary storage... [0s] +Building reference histograms... [0.01s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6032,7 +6068,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6060,7 +6096,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6088,7 +6124,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6120,7 +6156,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -6137,7 +6173,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6172,7 +6208,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6180,7 +6216,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6190,7 +6226,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -6200,11 +6236,11 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -6223,7 +6259,7 @@ Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.001s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -6249,7 +6285,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6312,7 +6348,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6362,7 +6398,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6411,12 +6447,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.009s] +Computing alignments... Loading trace points... [0.008s] Sorting trace points... [0s] -Computing alignments... [0.104s] +Computing alignments... [0.101s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.115s] + [0.111s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6426,17 +6462,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.671s +Total time = 0.681s Reported 489 pairwise alignments, 489 HSPs. 32 queries aligned. -+ diamond blastp --threads 1 --db test/M.faa.diamond --query test/E.faa --out /tmp/tmp.P8oDZbS2vc/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/M.faa.diamond --query test/E.faa --out /tmp/tmp.E9mgkFlIle/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -6444,32 +6480,32 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.006s] +Masking queries... [0.005s] Algorithm: Double-indexed -Building query histograms... [0.012s] +Building query histograms... [0.01s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.002s] -Initializing temporary storage... [0.004s] -Building reference histograms... [0.005s] +Initializing temporary storage... [0s] +Building reference histograms... [0.006s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6539,21 +6575,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6581,7 +6617,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6630,7 +6666,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6675,7 +6711,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. Building reference seed array... [0.001s] @@ -6687,16 +6723,16 @@ Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.001s] @@ -6721,7 +6757,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6729,7 +6765,7 @@ Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. Building reference seed array... [0.001s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -6749,14 +6785,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6773,11 +6809,11 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6799,7 +6835,7 @@ Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -6833,7 +6869,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6850,7 +6886,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -6889,7 +6925,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6903,12 +6939,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.008s] +Computing alignments... Loading trace points... [0.05s] Sorting trace points... [0s] -Computing alignments... [0.218s] +Computing alignments... [0.209s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.229s] + [0.262s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6918,17 +6954,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.781s +Total time = 0.817s Reported 1173 pairwise alignments, 1173 HSPs. 72 queries aligned. -+ diamond blastp --ignore-warnings --threads 1 --db test/E.faa.diamond --query test/C2.faa --out /tmp/tmp.P8oDZbS2vc/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --ignore-warnings --threads 1 --db test/E.faa.diamond --query test/C2.faa --out /tmp/tmp.E9mgkFlIle/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -6941,9 +6977,9 @@ Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] -Initializing temporary storage... [0.004s] -Building reference histograms... [0.011s] +Masking reference... [0.003s] +Initializing temporary storage... [0s] +Building reference histograms... [0.013s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -6953,21 +6989,21 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6981,7 +7017,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7093,14 +7129,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7121,7 +7157,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7149,7 +7185,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7212,11 +7248,11 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -7268,14 +7304,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7289,7 +7325,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7324,7 +7360,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7395,12 +7431,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.007s] +Computing alignments... Loading trace points... [0.001s] Sorting trace points... [0s] Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.009s] + [0.004s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7410,17 +7446,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.438s +Total time = 0.489s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/E.faa --out /tmp/tmp.P8oDZbS2vc/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/E.faa --out /tmp/tmp.E9mgkFlIle/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -7428,13 +7464,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.006s] +Masking queries... [0.005s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.011s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] -Initializing temporary storage... [0.005s] +Initializing temporary storage... [0.046s] Building reference histograms... [0s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -7442,18 +7478,18 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7488,7 +7524,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7537,7 +7573,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7558,14 +7594,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7593,7 +7629,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7648,7 +7684,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7698,14 +7734,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7726,7 +7762,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7754,21 +7790,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7782,7 +7818,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7810,14 +7846,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7873,7 +7909,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7887,12 +7923,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.007s] +Computing alignments... Loading trace points... [0.06s] Sorting trace points... [0s] Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.009s] + [0.062s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7902,17 +7938,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.437s +Total time = 0.591s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/L.faa.diamond --query test/M.faa --out /tmp/tmp.P8oDZbS2vc/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/L.faa.diamond --query test/M.faa --out /tmp/tmp.E9mgkFlIle/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -7920,14 +7956,14 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.009s] +Masking queries... [0.005s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.002s] -Initializing temporary storage... [0.005s] -Building reference histograms... [0.006s] +Masking reference... [0.001s] +Initializing temporary storage... [0s] +Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.001s] @@ -7990,14 +8026,14 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -8011,7 +8047,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [0.001s] @@ -8116,7 +8152,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0.001s] @@ -8228,7 +8264,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0.001s] @@ -8256,21 +8292,21 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -8326,7 +8362,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -8354,7 +8390,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -8365,7 +8401,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] @@ -8379,12 +8415,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.008s] +Computing alignments... Loading trace points... [0.003s] Sorting trace points... [0s] -Computing alignments... [0.072s] +Computing alignments... [0.07s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.082s] + [0.075s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8394,17 +8430,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.663s +Total time = 0.712s Reported 390 pairwise alignments, 390 HSPs. 39 queries aligned. -+ diamond blastp --threads 1 --db test/M.faa.diamond --query test/L.faa --out /tmp/tmp.P8oDZbS2vc/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/M.faa.diamond --query test/L.faa --out /tmp/tmp.E9mgkFlIle/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -8412,13 +8448,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.008s] +Masking queries... [0.005s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.002s] -Initializing temporary storage... [0.004s] +Initializing temporary storage... [0s] Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -8471,7 +8507,7 @@ Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8510,7 +8546,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -8520,7 +8556,7 @@ Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8538,14 +8574,14 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] -Computing hash join... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -8566,7 +8602,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [0.001s] @@ -8655,7 +8691,7 @@ Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] -Computing hash join... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] Deallocating memory... [0s] @@ -8689,7 +8725,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] @@ -8699,7 +8735,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0.001s] @@ -8713,14 +8749,14 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0.001s] @@ -8741,14 +8777,14 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. Building reference seed array... [0.001s] @@ -8760,13 +8796,13 @@ Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] @@ -8774,8 +8810,8 @@ Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0.001s] Building query seed array... [0.001s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0.001s] +Computing hash join... [0s] +Masking low complexity seeds... [0s] Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. @@ -8790,14 +8826,14 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -8839,7 +8875,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0.001s] @@ -8871,12 +8907,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.013s] +Computing alignments... Loading trace points... [0.016s] Sorting trace points... [0s] -Computing alignments... [0.073s] +Computing alignments... [0.076s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.089s] + [0.104s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8886,17 +8922,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.695s +Total time = 0.721s Reported 390 pairwise alignments, 390 HSPs. 40 queries aligned. -+ diamond blastp --ignore-warnings --threads 1 --db test/L.faa.diamond --query test/C2.faa --out /tmp/tmp.P8oDZbS2vc/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --ignore-warnings --threads 1 --db test/L.faa.diamond --query test/C2.faa --out /tmp/tmp.E9mgkFlIle/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -8906,11 +8942,11 @@ Loading query sequences... [0s] Masking queries... [0s] Algorithm: Double-indexed -Building query histograms... [0.001s] +Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.002s] -Initializing temporary storage... [0.006s] +Initializing temporary storage... [0s] Building reference histograms... [0.005s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -8918,17 +8954,17 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9019,7 +9055,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9363,12 +9399,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.006s] +Computing alignments... Loading trace points... [0s] Sorting trace points... [0s] Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.008s] + [0.002s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9378,17 +9414,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.342s +Total time = 0.413s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/L.faa --out /tmp/tmp.P8oDZbS2vc/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/L.faa --out /tmp/tmp.E9mgkFlIle/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -9396,13 +9432,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.008s] +Masking queries... [0.005s] Algorithm: Double-indexed Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] -Initializing temporary storage... [0.005s] +Initializing temporary storage... [0s] Building reference histograms... [0s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -9410,14 +9446,14 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0s] @@ -9526,7 +9562,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9617,7 +9653,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9765,7 +9801,7 @@ Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0s] Building query seed array... [0.001s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -9795,7 +9831,7 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. Building reference seed array... [0s] @@ -9855,12 +9891,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.006s] +Computing alignments... Loading trace points... [0.001s] Sorting trace points... [0s] Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.009s] + [0.002s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9870,17 +9906,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.363s +Total time = 0.366s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --ignore-warnings --threads 1 --db test/M.faa.diamond --query test/C2.faa --out /tmp/tmp.P8oDZbS2vc/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --ignore-warnings --threads 1 --db test/M.faa.diamond --query test/C2.faa --out /tmp/tmp.E9mgkFlIle/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -9888,28 +9924,28 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.001s] +Masking queries... [0s] Algorithm: Double-indexed Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.002s] -Initializing temporary storage... [0.006s] -Building reference histograms... [0.005s] +Initializing temporary storage... [0.002s] +Building reference histograms... [0.006s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.001s] @@ -10080,7 +10116,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10220,7 +10256,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10347,12 +10383,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.009s] +Computing alignments... Loading trace points... [0.033s] Sorting trace points... [0s] Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.011s] + [0.035s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10362,17 +10398,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.361s +Total time = 0.395s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/M.faa --out /tmp/tmp.P8oDZbS2vc/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive ++ diamond blastp --threads 1 --db test/C2.faa.diamond --query test/M.faa --out /tmp/tmp.E9mgkFlIle/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.9.163 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021) #CPU threads: 1 Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) -Temporary directory: /tmp/tmp.P8oDZbS2vc +Temporary directory: /tmp/tmp.E9mgkFlIle #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -10380,13 +10416,13 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.01s] +Masking queries... [0.005s] Algorithm: Double-indexed -Building query histograms... [0.006s] +Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] -Initializing temporary storage... [0.009s] +Initializing temporary storage... [0.005s] Building reference histograms... [0s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. @@ -10394,14 +10430,14 @@ Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0s] @@ -10839,12 +10875,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.006s] +Computing alignments... Loading trace points... [0s] Sorting trace points... [0s] Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.008s] + [0.002s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10854,10 +10890,10 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.384s +Total time = 0.366s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ rm -rf /tmp/tmp.P8oDZbS2vc ++ rm -rf /tmp/tmp.E9mgkFlIle make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9' create-stamp debian/debhelper-build-stamp dh_prep @@ -10903,12 +10939,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/2386646/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2386646/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/982005 and its subdirectories -I: Current time: Thu Jul 3 02:53:49 -12 2025 -I: pbuilder-time-stamp: 1751554429 +I: removing directory /srv/workspace/pbuilder/2386646 and its subdirectories +I: Current time: Fri May 31 22:34:08 +14 2024 +I: pbuilder-time-stamp: 1717144448