Diff of the two buildlogs: -- --- b1/build.log 2025-01-07 16:17:41.649075168 +0000 +++ b2/build.log 2025-01-07 16:22:50.123022228 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Tue Jan 7 04:12:43 -12 2025 -I: pbuilder-time-stamp: 1736266363 +I: Current time: Tue Feb 10 12:40:57 +14 2026 +I: pbuilder-time-stamp: 1770676857 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration @@ -26,52 +26,84 @@ 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/1541781/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/233616/tmp/hooks/D01_modify_environment starting +debug: Running on codethink01-arm64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Feb 9 22:41 /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/233616/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/233616/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='arm64' - 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]="37" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.2.37(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=arm64 + DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' - DISTRIBUTION='trixie' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=trixie + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='a7b0c6dfd6d4409fba84775203811d41' - 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='1541781' - PS1='# ' - PS2='> ' + INVOCATION_ID=f95303b70cce4eabb31a0a58335cde5c + LANG=C + LANGUAGE=nl_BE:nl + LC_ALL=C + MACHTYPE=aarch64-unknown-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=233616 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.v9D2oEqv/pbuilderrc_vjTJ --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.v9D2oEqv/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' - http_proxy='http://192.168.101.4:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.v9D2oEqv/pbuilderrc_ttIO --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.v9D2oEqv/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' + http_proxy=http://192.168.101.4:3128 I: uname -a - Linux codethink04-arm64 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-28-cloud-arm64 #1 SMP Debian 6.1.119-1 (2024-11-22) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1541781/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/233616/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -167,7 +199,7 @@ Get: 52 http://deb.debian.org/debian trixie/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 53 http://deb.debian.org/debian trixie/main arm64 debhelper all 13.23 [919 kB] Get: 54 http://deb.debian.org/debian trixie/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 36.0 MB in 0s (168 MB/s) +Fetched 36.0 MB in 0s (191 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:arm64. (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 ... 20097 files and directories currently installed.) @@ -398,7 +430,11 @@ 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/233616/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for trixie +I: user script /srv/workspace/pbuilder/233616/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 @@ -455,8 +491,8 @@ -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE --- Configuring done (2.2s) --- Generating done (0.0s) +-- Configuring done (2.8s) +-- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: @@ -482,46 +518,42 @@ make -f CMakeFiles/arch_neon.dir/build.make CMakeFiles/arch_neon.dir/depend make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu' -cd /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu/CMakeFiles/arch_generic.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu/CMakeFiles/arch_neon.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-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-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu/CMakeFiles/arch_generic.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-linux-gnu' make -f 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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 -mbranch-protection=standard -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/dp/pfscan/pfscan.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/pfscan/pfscan.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/pfscan/pfscan.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/pfscan/pfscan.cpp -[ 9%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o +[ 8%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK 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CMakeFiles/arch_neon.dir/src/dp/swipe/anchored_wrapper.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/dp/swipe/anchored_wrapper.cpp.o -MF CMakeFiles/arch_neon.dir/src/dp/swipe/anchored_wrapper.cpp.o.d -o CMakeFiles/arch_neon.dir/src/dp/swipe/anchored_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/anchored_wrapper.cpp +[ 9%] Building CXX object CMakeFiles/arch_neon.dir/src/dp/score_profile.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/dp/score_profile.cpp.o -MF CMakeFiles/arch_neon.dir/src/dp/score_profile.cpp.o.d -o CMakeFiles/arch_neon.dir/src/dp/score_profile.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/dp/score_profile.cpp [ 10%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/dp/score_profile.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o.d -o CMakeFiles/arch_generic.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++/14/list:62, @@ -671,12 +707,11 @@ /usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 952 | *__first = __tmp; | ~~~~~~~~~^~~~~~~ -In file included from /usr/include/c++/14/list:62, - from /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:22: In function ‘typename __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:998:21, inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:1029:20, - inlined from ‘DP::Swipe::ARCH_NEON::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:64:12: + inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:64:12, + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:155:9: /usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 952 | *__first = __tmp; | ~~~~~~~~~^~~~~~~ @@ -684,15 +719,16 @@ inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:998:21, inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:1029:20, inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:64:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:155:9: + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:155:9: /usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 952 | *__first = __tmp; | ~~~~~~~~~^~~~~~~ +In file included from /usr/include/c++/14/list:62, + from /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/swipe_wrapper.cpp:22: In function ‘typename __gnu_cxx::__enable_if::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, inlined from ‘void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:998:21, inlined from ‘void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/14/bits/stl_algobase.h:1029:20, - inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:64:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, _cbs, std::vector&, DP::Params&) [with _sv = int; _cbs = DP::NoCBS; It = __gnu_cxx::__normal_iterator >; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_swipe.h:155:9: + inlined from ‘DP::Swipe::ARCH_NEON::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.9/src/dp/swipe/full_matrix.h:64:12: /usr/include/c++/14/bits/stl_algobase.h:952:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 952 | 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-DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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_random.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/njn_random.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/njn_random.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/njn_random.cpp [ 60%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/sls_alignment_evaluer.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/sls_alignment_evaluer.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_alignment_evaluer.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_alignment_evaluer.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_alignment_evaluer.cpp [ 60%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/sls_alp.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/sls_alp.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_alp.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_alp.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_alp.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/sls_alp_data.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/sls_alp_data.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_alp_data.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_alp_data.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_alp_data.cpp 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=] @@ -973,6 +1007,8 @@ /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 ( | ^~~~ +[ 61%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/sls_alp_data.cpp.o +/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/sls_alp_data.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_alp_data.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_alp_data.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_alp_data.cpp 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_localmaxstat.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=] @@ -993,14 +1029,14 @@ /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 [ 62%] 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 -DWITH_NEON -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 -mbranch-protection=standard -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/sls_alp_regression.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_alp_regression.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_alp_regression.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_alp_regression.cpp +cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics [ 62%] Building CXX object CMakeFiles/diamond.dir/src/lib/alp/sls_alp_sim.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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 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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 -MD -MT CMakeFiles/diamond.dir/src/lib/alp/sls_pvalues.cpp.o -MF CMakeFiles/diamond.dir/src/lib/alp/sls_pvalues.cpp.o.d -o CMakeFiles/diamond.dir/src/lib/alp/sls_pvalues.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/lib/alp/sls_pvalues.cpp [ 64%] Building CXX object CMakeFiles/diamond.dir/src/align/global_ranking/global_ranking.cpp.o @@ -1119,9 +1155,9 @@ /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/cluster/cascaded/helpers.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cascaded/helpers.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/cluster/cascaded/helpers.cpp [ 95%] Building CXX object CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/cluster/cascaded/wrapper.cpp.o -MF CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o.d -o CMakeFiles/diamond.dir/src/cluster/cascaded/wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/cluster/cascaded/wrapper.cpp -[ 95%] Building CXX object CMakeFiles/diamond.dir/src/chaining/backtrace.cpp.o [ 96%] Building CXX object CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/output/daa/merge.cpp.o -MF CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o.d -o CMakeFiles/diamond.dir/src/output/daa/merge.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/output/daa/merge.cpp +[ 96%] Building CXX object CMakeFiles/diamond.dir/src/chaining/backtrace.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/chaining/backtrace.cpp.o -MF CMakeFiles/diamond.dir/src/chaining/backtrace.cpp.o.d -o CMakeFiles/diamond.dir/src/chaining/backtrace.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/chaining/backtrace.cpp [ 97%] Building CXX object CMakeFiles/diamond.dir/src/util/tsv/merge.cpp.o /usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -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 -mbranch-protection=standard -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/util/tsv/merge.cpp.o -MF CMakeFiles/diamond.dir/src/util/tsv/merge.cpp.o.d -o CMakeFiles/diamond.dir/src/util/tsv/merge.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.9/src/util/tsv/merge.cpp @@ -1143,17 +1179,17 @@ make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9/obj-aarch64-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-aarch64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games sh diamond-calls -+ mktemp -d -+ TESTDIR=/tmp/tmp.td2dDWEXlJ -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.td2dDWEXlJ/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-aarch64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path sh diamond-calls +++ mktemp -d ++ TESTDIR=/tmp/tmp.wSZbnPk58M ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -1161,136 +1197,136 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.008s] +Masking queries... [0.009s] Algorithm: Double-indexed -Building query histograms... [0.009s] +Building query histograms... [0.038s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.022s] +Building reference histograms... [0.026s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.007s] +Computing hash join... [0.001s] 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... [0.004s] -Building query seed array... [0.007s] +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 1/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.001s] +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 1/16, index chunk 4/4. Building reference seed array... [0.006s] -Building query seed array... [0.006s] +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 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.015s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] 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 query seed array... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0.004s] -Searching alignments... [0.003s] +Masking low complexity seeds... [0s] +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... [0.004s] +Building reference seed array... [0.001s] 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 2/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. 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... [0s] 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 query 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... [0s] 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... [0.001s] -Computing hash join... [0.002s] +Building query seed array... [0.002s] +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 3/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.006s] +Building reference seed array... [0.011s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.002s] Searching alignments... [0s] 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... [0.002s] +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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.014s] +Computing hash join... [0.002s] 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... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] 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 query seed array... [0.003s] +Building reference seed array... [0.006s] +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 1/4. 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... [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... [0.017s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1301,24 +1337,24 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] 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 query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.003s] 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... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1339,37 +1375,37 @@ Searching alignments... [0s] Deallocating memory... [0s] 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... [0.003s] +Building reference seed array... [0.001s] +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 7/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.002s] +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 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building query seed array... [0.008s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -1382,7 +1418,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.015s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1409,7 +1445,7 @@ 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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -1423,29 +1459,29 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] 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 10/16, index chunk 2/4. -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] -Searching alignments... [0.001s] +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 query seed array... [0.003s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] 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 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -1455,177 +1491,177 @@ Building query seed array... [0.002s] 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 11/16, 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... [0s] +Searching alignments... [0.003s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.005s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.001s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] 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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.008s] +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 12/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 12/16, index chunk 4/4. -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] 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... [0.002s] -Building query 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... [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 query 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... [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... [0.003s] +Building reference seed array... [0.001s] +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 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building reference seed array... [0.001s] +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 14/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query 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... [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... [0.001s] +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 14/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.005s] +Building reference seed array... [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 15/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.003s] +Building reference seed array... [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 15/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.003s] +Building reference seed array... [0.001s] +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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] 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 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.001s] Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.001s] 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... [0.005s] -Building query seed array... [0.006s] +Building reference seed array... [0.002s] +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 16/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +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 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] +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... [0.004s] +Computing alignments... Loading trace points... [0.005s] Sorting trace points... [0s] Computing alignments... [0.19s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.196s] + [0.197s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -1635,17 +1671,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.91s +Total time = 0.973s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -1655,458 +1691,458 @@ Loading query sequences... [0s] Masking queries... [0.024s] Algorithm: Double-indexed -Building query histograms... [0.033s] +Building query histograms... [0.008s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.011s] +Building reference histograms... [0.009s] 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... [0.004s] +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... [0.003s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] +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 1/16, 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... [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... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] +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 2/16, index chunk 2/4. Building reference seed array... [0.004s] -Building query seed array... [0.004s] +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 2/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query 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 2/16, index chunk 4/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 3/16, index chunk 3/4. Building reference seed array... [0.003s] -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 3/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.01s] +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 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.006s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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... [0.004s] -Building query seed array... [0.005s] +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 4/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.002s] Building query seed array... [0.003s] -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 5/16, index chunk 1/4. -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] 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 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 5/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.004s] +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 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference 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 6/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.004s] +Building reference seed array... [0.002s] +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... [0.004s] -Computing hash join... [0.001s] +Building reference 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 6/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.021s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 7/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.007s] +Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.005s] -Building query seed array... [0.005s] +Building reference seed array... [0.002s] +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 7/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 8/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference 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 8/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference 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 8/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 9/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [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] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 9/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.004s] +Building reference seed array... [0.005s] +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 9/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 10/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.002s] Building query seed array... [0.003s] -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 10/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 10/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 10/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] +Computing hash join... [0s] +Masking low complexity seeds... [0.002s] 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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] +Computing hash join... [0.018s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 12/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] +Building reference seed array... [0.002s] +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 12/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 12/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 13/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0.001s] 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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 15/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +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 15/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 15/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0s] +Masking low complexity seeds... [0.001s] 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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference 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... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -2114,10 +2150,10 @@ Clearing query masking... [0s] Computing alignments... Loading trace points... [0.002s] Sorting trace points... [0s] -Computing alignments... [0.075s] -Deallocating buffers... [0s] +Computing alignments... [0.033s] +Deallocating buffers... [0.002s] Loading trace points... [0s] - [0.079s] + [0.038s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -2127,17 +2163,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.139s +Total time = 0.734s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -2145,199 +2181,199 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.024s] +Masking queries... [0.019s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.008s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.024s] +Building reference histograms... [0.011s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.005s] -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 1/16, index chunk 2/4. -Building reference seed array... [0.004s] -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 1/16, index chunk 3/4. -Building reference seed array... [0.005s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 2/16, index chunk 2/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.002s] 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 3/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query 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 3/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +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 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +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 4/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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... [0.004s] -Building query seed array... [0.002s] +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 5/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.003s] +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 5/16, index chunk 2/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query 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 5/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query 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 6/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.003s] 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 6/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +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 7/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] +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 7/16, index chunk 2/4. -Building reference seed array... [0.005s] +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 7/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2345,83 +2381,83 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0.004s] -Building query seed array... [0.002s] +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 1/4. -Building reference seed array... [0.005s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query 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... [0.004s] +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 8/16, index chunk 4/4. -Building reference seed array... [0.004s] -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] +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... [0.004s] +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 9/16, index chunk 2/4. -Building reference seed array... [0.004s] -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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.004s] +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 9/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query 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 10/16, index chunk 1/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] 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 10/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2435,49 +2471,49 @@ 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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] +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 11/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +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 3/4. -Building reference seed array... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] 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 12/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +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 12/16, index chunk 2/4. -Building reference seed array... [0.004s] +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 12/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2491,22 +2527,22 @@ 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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +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 13/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.003s] 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 13/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query 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] @@ -2534,41 +2570,41 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.003s] +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 14/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.003s] -Computing hash join... [0s] +Computing hash join... [0.001s] 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... [0.005s] Building query seed array... [0.003s] -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 15/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.001s] 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... [0.005s] 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 15/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2576,24 +2612,24 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.009s] +Building query seed array... [0.003s] +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 16/16, index chunk 2/4. -Building reference seed array... [0.004s] +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 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. Building reference seed array... [0.004s] @@ -2604,12 +2640,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.003s] +Computing alignments... Loading trace points... [0.004s] Sorting trace points... [0s] -Computing alignments... [0.127s] +Computing alignments... [0.12s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.132s] + [0.125s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -2619,17 +2655,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.087s +Total time = 0.883s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -2637,18 +2673,18 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.028s] +Masking queries... [0.029s] Algorithm: Double-indexed -Building query histograms... [0.023s] +Building query histograms... [0.016s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +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... [0.003s] -Building query seed array... [0.004s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -2658,34 +2694,34 @@ Building query seed array... [0.004s] 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... [0.004s] +Building reference seed array... [0.001s] +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 1/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.004s] 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 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +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 2/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.001s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. @@ -2697,14 +2733,14 @@ 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... [0.004s] -Computing hash join... [0.001s] +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 3/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2717,51 +2753,51 @@ 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... [0.001s] +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 3/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] +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 4/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.004s] +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 4/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building query seed array... [0.005s] +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 query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.004s] +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 4/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.007s] 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 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -2773,14 +2809,14 @@ 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... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] 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 4/4. -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] @@ -2788,8 +2824,8 @@ 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 query seed array... [0.005s] -Computing hash join... [0.001s] +Building query seed array... [0.004s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -2801,113 +2837,113 @@ 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... [0.001s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] +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 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.004s] -Computing hash join... [0s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] 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 query seed array... [0.004s] +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 7/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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... [0.004s] +Building reference seed array... [0.005s] +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 8/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building query seed array... [0.005s] +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 8/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building query seed array... [0.005s] +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 query seed array... [0.004s] +Building reference seed array... [0.001s] +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 8/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.008s] +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 9/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.004s] 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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.004s] +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 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] 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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.006s] +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 10/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.004s] 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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2915,7 +2951,7 @@ Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.004s] -Computing hash join... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -2935,7 +2971,7 @@ 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 query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -2943,33 +2979,33 @@ 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... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.001s] 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... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 12/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.003s] 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 12/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +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 12/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -2977,56 +3013,56 @@ 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 query seed array... [0.005s] +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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] 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 13/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.003s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.004s] +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 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] 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 14/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3034,55 +3070,55 @@ Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.003s] -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 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +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 15/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.003s] +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 15/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.005s] +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 16/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.005s] +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 16/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +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... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3090,18 +3126,18 @@ 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... [0.004s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.005s] +Computing alignments... Loading trace points... [0.004s] Sorting trace points... [0s] -Computing alignments... [0.195s] +Computing alignments... [0.172s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.201s] + [0.178s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3111,17 +3147,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.103s +Total time = 1.05s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -3129,18 +3165,18 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.021s] +Masking queries... [0.025s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.01s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.007s] Initializing temporary storage... [0s] -Building reference histograms... [0.025s] +Building reference histograms... [0.024s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.005s] -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] @@ -3150,7 +3186,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.004s] @@ -3160,15 +3196,15 @@ 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... [0.005s] -Building query seed array... [0.003s] +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 2/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3181,7 +3217,7 @@ 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... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3189,41 +3225,41 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. Building reference seed array... [0.004s] -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 3/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 3/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 3/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] +Building reference seed array... [0.007s] +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 3/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] 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 4/16, index chunk 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3232,47 +3268,47 @@ Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.005s] 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 4/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 4/4. -Building reference seed array... [0.004s] +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 5/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.004s] -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 5/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query 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 5/16, index chunk 4/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3286,16 +3322,16 @@ 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... [0.004s] +Building reference seed array... [0.005s] 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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -3307,56 +3343,56 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.004s] +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 7/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 7/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 7/16, index chunk 4/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 8/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 8/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 8/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] 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 8/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3370,7 +3406,7 @@ 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... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3391,7 +3427,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3405,14 +3441,14 @@ 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... [0.004s] +Building reference seed array... [0.005s] 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 10/16, index chunk 4/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3426,57 +3462,57 @@ 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... [0.018s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.005s] +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... [0.005s] +Building reference seed array... [0.004s] 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 11/16, index chunk 4/4. -Building reference seed array... [0.017s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.004s] +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 12/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] 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... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] -Computing hash join... [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 12/16, index chunk 3/4. Building reference seed array... [0.005s] -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... [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 query seed array... [0.001s] -Computing hash join... [0.001s] +Building reference seed array... [0.005s] +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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3486,46 +3522,46 @@ 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 13/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.003s] -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 13/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.004s] +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 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 14/16, index chunk 2/4. Building reference seed array... [0.005s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.004s] +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 4/4. -Building reference seed array... [0.004s] -Building query 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] @@ -3538,14 +3574,14 @@ 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... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] -Computing hash join... [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 15/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3553,20 +3589,20 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0.005s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.004s] +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 16/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3590,10 +3626,10 @@ Clearing query masking... [0s] Computing alignments... Loading trace points... [0.003s] Sorting trace points... [0s] -Computing alignments... [0.116s] +Computing alignments... [0.125s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.121s] + [0.13s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3603,17 +3639,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.137s +Total time = 1.05s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -3621,9 +3657,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.025s] +Masking queries... [0.029s] Algorithm: Double-indexed -Building query histograms... [0.024s] +Building query histograms... [0.025s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.004s] @@ -3639,21 +3675,21 @@ 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... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [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 query seed array... [0.005s] -Computing hash join... [0.001s] +Building query seed array... [0.004s] +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 query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3681,17 +3717,17 @@ 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... [0.005s] +Building query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.004s] 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... [0.002s] @@ -3709,8 +3745,8 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building query seed array... [0.005s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -3723,49 +3759,49 @@ 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 query seed array... [0.004s] +Building query seed array... [0.005s] 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 query seed array... [0.004s] +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 4/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.004s] -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 5/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.005s] +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 query seed array... [0.003s] -Computing hash join... [0s] +Building query seed array... [0.004s] +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 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3778,14 +3814,14 @@ 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... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] 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... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3799,43 +3835,43 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.004s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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 query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.002s] -Building query seed array... [0.005s] +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 7/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] 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 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building query seed array... [0.005s] +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 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3843,7 +3879,7 @@ 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... [0.004s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -3855,15 +3891,15 @@ 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... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.003s] +Building query seed array... [0.005s] 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 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3871,47 +3907,47 @@ Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.004s] -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 9/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] 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 10/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.004s] 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 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.004s] 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 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -3919,14 +3955,14 @@ 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 query seed array... [0.003s] +Building query seed array... [0.004s] 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... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3940,7 +3976,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -3955,69 +3991,69 @@ Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.004s] -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 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.005s] +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 13/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.006s] 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 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +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... [0.002s] -Building query seed array... [0.004s] +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 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +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 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [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] -Building query seed array... [0.005s] +Building query seed array... [0.004s] 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... [0.004s] +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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.003s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4031,13 +4067,13 @@ 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... [0.004s] +Building query seed array... [0.005s] 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... [0.008s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4052,14 +4088,14 @@ 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 query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.004s] +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 16/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4080,12 +4116,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.003s] Sorting trace points... [0s] -Computing alignments... [0.202s] +Computing alignments... [0.194s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.208s] + [0.198s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4095,17 +4131,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.143s +Total time = 1.144s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -4118,9 +4154,9 @@ Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.008s] +Masking reference... [0.004s] Initializing temporary storage... [0s] -Building reference histograms... [0.024s] +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... [0.005s] @@ -4134,7 +4170,7 @@ 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 1/16, index chunk 3/4. Building reference seed array... [0.003s] @@ -4144,14 +4180,14 @@ 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... [0.004s] +Building reference seed array... [0.005s] 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 2/16, index chunk 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4165,42 +4201,42 @@ 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... [0.005s] +Building reference seed array... [0.004s] 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 2/16, index chunk 4/4. -Building reference seed array... [0.004s] +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 3/16, index chunk 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.001s] 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 3/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.002s] 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 3/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] 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 3/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4214,80 +4250,80 @@ 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... [0.005s] +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 4/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] 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... [0.005s] Building query seed array... [0s] 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... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.018s] +Building query seed array... [0.023s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.018s] +Building query seed array... [0.023s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.03s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.015s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.002s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. @@ -4312,272 +4348,272 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.001s] 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 8/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.031s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] 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 query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.018s] +Building query seed array... [0.031s] +Computing hash join... [0.012s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.027s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.019s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.027s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.029s] +Building query seed array... [0.023s] +Computing hash join... [0.016s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.014s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.018s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.022s] +Building query seed array... [0.019s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.039s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.035s] +Computing hash join... [0.016s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.023s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.024s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.034s] +Building query seed array... [0.028s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.017s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.043s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.016s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.003s] 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... [0.004s] +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... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.015s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.035s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.001s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.026s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.016s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.029s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.017s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.022s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.024s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.027s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.013s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.022s] +Building query seed array... [0.019s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.017s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0.034s] Sorting trace points... [0s] -Computing alignments... [0.004s] -Deallocating buffers... [0s] +Computing alignments... [0.011s] +Deallocating buffers... [0.007s] Loading trace points... [0s] - [0.007s] + [0.055s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4587,17 +4623,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.727s +Total time = 4.548s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -4605,9 +4641,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.03s] +Masking queries... [0.02s] Algorithm: Double-indexed -Building query histograms... [0.025s] +Building query histograms... [0.018s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -4622,454 +4658,454 @@ 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... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.014s] +Building query seed array... [0.019s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.013s] +Searching alignments... [0.012s] 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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.032s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.026s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] 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... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.019s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.023s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.026s] +Building query seed array... [0.009s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] 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... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.027s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.019s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.006s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.027s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.027s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.015s] 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... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.031s] +Building query seed array... [0.027s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.027s] +Building query seed array... [0.019s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.02s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.018s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.033s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.01s] 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 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.014s] +Building query seed array... [0.015s] +Computing hash join... [0.019s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.015s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.03s] +Building query seed array... [0.007s] +Computing hash join... [0.011s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.009s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.005s] +Computing hash join... [0.012s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.002s] 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... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.016s] +Building query seed array... [0.031s] +Computing hash join... [0.015s] +Masking low complexity seeds... [0.015s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.023s] +Building query seed array... [0.023s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.026s] +Building query seed array... [0.002s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.012s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.005s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0s] -Building query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 2/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +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... [0s] -Building query seed array... [0.004s] +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 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.005s] +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 9/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 9/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.001s] +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 9/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.006s] 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 4/4. -Building reference seed array... [0s] +Building reference seed array... [0.005s] Building query seed array... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Computing hash join... [0s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.006s] 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 2/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 10/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 10/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 2/4. Building reference seed array... [0s] -Building query 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 3/4. Building reference seed array... [0s] -Building query 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... [0s] -Building query 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 12/16, index chunk 1/4. Building reference seed array... [0s] -Building query 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 12/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 12/16, index chunk 3/4. -Building reference seed array... [0s] -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... [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 reference seed array... [0.002s] 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 1/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] 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... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.007s] 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... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.004s] 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 4/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0.001s] +Masking low complexity seeds... [0s] 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... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.01s] +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... [0s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building query seed array... [0.009s] +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... [0.008s] -Computing hash join... [0.003s] -Masking low complexity seeds... [0.003s] -Searching alignments... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0s] +Masking low complexity seeds... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.008s] 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... [0.004s] +Building reference seed array... [0s] +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 15/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +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 4/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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... [0s] -Building query seed array... [0.004s] +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 16/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0s] +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 16/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 16/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +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] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0s] Sorting trace points... [0s] -Computing alignments... [0.004s] +Computing alignments... [0.001s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.009s] + [0.003s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5079,17 +5115,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.863s +Total time = 2.347s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -5097,471 +5133,471 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.022s] +Masking queries... [0.018s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.005s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.007s] +Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.026s] +Building reference histograms... [0.009s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.005s] -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... [0.002s] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] 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 3/4. -Building reference seed array... [0.005s] -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 1/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query 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... [0.001s] +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... [0.004s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference 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 2/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query 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 2/16, index chunk 4/4. -Building reference seed array... [0.005s] -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 3/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building reference seed array... [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 3/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +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 3/16, index chunk 3/4. -Building reference seed array... [0.005s] -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 3/16, index chunk 4/4. -Building reference seed array... [0.004s] -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 4/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [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 4/16, index chunk 3/4. -Building reference seed array... [0.009s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [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 4/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +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 5/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +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 5/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +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... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0.001s] 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... [0.005s] +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 1/4. -Building reference seed array... [0.005s] +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 6/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] 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 3/4. -Building reference seed array... [0.004s] -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 6/16, index chunk 4/4. -Building reference seed array... [0.005s] -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 7/16, index chunk 1/4. -Building reference seed array... [0.005s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +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 7/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query 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... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.005s] -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 8/16, index chunk 2/4. -Building reference seed array... [0.005s] -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 8/16, index chunk 3/4. -Building reference seed array... [0.005s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.005s] -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 9/16, index chunk 1/4. -Building reference seed array... [0.005s] -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 9/16, index chunk 2/4. -Building reference seed array... [0.005s] -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 9/16, index chunk 3/4. -Building reference seed array... [0.005s] +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... [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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query 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 10/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +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 3/4. -Building reference seed array... [0.005s] -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... [0.005s] +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 11/16, index chunk 1/4. -Building reference seed array... [0.005s] -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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4. -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] +Masking low complexity seeds... [0.001s] +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... [0.005s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.005s] -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 12/16, index chunk 1/4. -Building reference seed array... [0.005s] -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 12/16, index chunk 2/4. -Building reference seed array... [0.005s] -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 12/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.005s] -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 13/16, index chunk 1/4. -Building reference seed array... [0.005s] -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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.005s] -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 13/16, index chunk 3/4. -Building reference seed array... [0.005s] -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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.005s] -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 14/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query 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 14/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.004s] +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 3/4. -Building reference seed array... [0.005s] -Building query 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 14/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0.005s] +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 15/16, index chunk 1/4. -Building reference seed array... [0.005s] -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 15/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.003s] 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 15/16, index chunk 3/4. -Building reference seed array... [0.001s] +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 15/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.001s] +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 16/16, index chunk 1/4. -Building reference seed array... [0.005s] +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... [0.001s] +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... [0.005s] +Building reference 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 16/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] +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] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.003s] Sorting trace points... [0s] -Computing alignments... [0.337s] +Computing alignments... [0.294s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.342s] + [0.299s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5571,17 +5607,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.359s +Total time = 0.868s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -5589,9 +5625,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.008s] +Masking queries... [0.009s] Algorithm: Double-indexed -Building query histograms... [0.026s] +Building query histograms... [0.025s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.004s] @@ -5599,8 +5635,8 @@ 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] -Building query seed array... [0.005s] +Building reference seed array... [0.003s] +Building query seed array... [0.004s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] @@ -5608,14 +5644,14 @@ 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... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] 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... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5627,7 +5663,7 @@ Searching alignments... [0.001s] 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... [0.003s] Building query seed array... [0.005s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] @@ -5649,22 +5685,22 @@ 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... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [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... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5692,7 +5728,7 @@ Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5706,16 +5742,16 @@ Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] 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 1/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. Building reference seed array... [0.002s] @@ -5727,28 +5763,28 @@ Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] 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 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] 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... [0.005s] -Computing hash join... [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 6/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5762,7 +5798,7 @@ Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5804,7 +5840,7 @@ Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5816,25 +5852,25 @@ Searching alignments... [0.001s] 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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [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... [0.002s] Building query seed array... [0.005s] -Computing hash join... [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] -Building query seed array... [0.005s] +Building query seed array... [0.004s] 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... [0.002s] @@ -5845,7 +5881,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5858,7 +5894,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5867,14 +5903,14 @@ Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [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] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5883,12 +5919,12 @@ Building query seed array... [0.005s] 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 query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -5897,10 +5933,10 @@ Building query seed array... [0.004s] 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 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5908,35 +5944,35 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0.001s] 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... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0.001s] 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... [0.002s] Building query seed array... [0.005s] 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 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5944,27 +5980,27 @@ 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... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] 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... [0.005s] +Building query seed array... [0.006s] 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 13/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] 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... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -5972,9 +6008,9 @@ 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... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] 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 3/4. Building reference seed array... [0.002s] @@ -5999,7 +6035,7 @@ 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... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6007,14 +6043,14 @@ 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... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] 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... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6027,7 +6063,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6035,14 +6071,14 @@ Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] 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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.006s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6050,10 +6086,10 @@ Clearing query masking... [0s] Computing alignments... Loading trace points... [0.004s] Sorting trace points... [0s] -Computing alignments... [0.603s] +Computing alignments... [0.578s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.609s] + [0.584s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6063,17 +6099,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.621s +Total time = 1.567s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -6098,21 +6134,21 @@ Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] 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 4/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] @@ -6121,19 +6157,19 @@ Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [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 2/16, index chunk 2/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6142,7 +6178,7 @@ Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6151,7 +6187,7 @@ 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 3/16, index chunk 2/4. Building reference seed array... [0.005s] @@ -6162,7 +6198,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0.005s] -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] @@ -6170,7 +6206,7 @@ Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6184,28 +6220,28 @@ Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [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... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] 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 1/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6219,7 +6255,7 @@ Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6232,7 +6268,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6268,20 +6304,20 @@ Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6302,36 +6338,36 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. Building reference seed array... [0.005s] -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 8/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [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 9/16, index chunk 2/4. Building reference seed array... [0.005s] -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 3/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6351,7 +6387,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. Building reference seed array... [0.005s] -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] @@ -6371,22 +6407,22 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query 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 11/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.003s] 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 11/16, index chunk 3/4. -Building reference seed array... [0.005s] -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... [0.001s] @@ -6400,21 +6436,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. Building reference seed array... [0.005s] -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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] 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... [0.005s] -Building query 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] @@ -6427,7 +6463,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6450,7 +6486,7 @@ Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0.005s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6459,14 +6495,14 @@ 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 14/16, index chunk 2/4. Building reference seed array... [0.005s] 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 14/16, index chunk 3/4. Building reference seed array... [0.005s] @@ -6508,7 +6544,7 @@ 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 16/16, index chunk 1/4. Building reference seed array... [0.005s] @@ -6519,17 +6555,17 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. Building reference seed array... [0.005s] -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] +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... [0.005s] 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 16/16, index chunk 4/4. Building reference seed array... [0.005s] @@ -6542,10 +6578,10 @@ Clearing query masking... [0s] Computing alignments... Loading trace points... [0.003s] Sorting trace points... [0s] -Computing alignments... [0.351s] +Computing alignments... [0.329s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.357s] + [0.334s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6555,17 +6591,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.379s +Total time = 1.351s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -6575,17 +6611,17 @@ Loading query sequences... [0s] Masking queries... [0.015s] Algorithm: Double-indexed -Building query histograms... [0.015s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.007s] +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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.002s] Deallocating memory... [0s] @@ -6597,64 +6633,64 @@ Searching alignments... [0.002s] 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... [0.005s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.002s] 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 query seed array... [0.004s] -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 2/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.002s] 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 query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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 query seed array... [0.005s] +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 2/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +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 3/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] -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 3/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] 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 3/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.006s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6667,8 +6703,8 @@ 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... [0.003s] -Building query seed array... [0.005s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6681,14 +6717,14 @@ Searching alignments... [0.001s] 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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.006s] +Computing hash join... [0.001s] Masking low complexity seeds... [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] +Building reference seed array... [0.003s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6697,34 +6733,34 @@ 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... [0.005s] -Computing hash join... [0.001s] +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 5/16, index chunk 2/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [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 3/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [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 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.006s] 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 6/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.01s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6732,7 +6768,7 @@ 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... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6745,14 +6781,14 @@ 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 query seed array... [0.005s] -Computing hash join... [0.001s] +Building query seed array... [0.003s] +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 7/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6766,7 +6802,7 @@ 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... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6774,14 +6810,14 @@ 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... [0.005s] -Computing hash join... [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 8/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6794,7 +6830,7 @@ 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... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6814,35 +6850,35 @@ Searching alignments... [0.001s] Deallocating memory... [0s] 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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] +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 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6850,8 +6886,8 @@ 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 query seed array... [0.003s] -Computing hash join... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6864,50 +6900,50 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] 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... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] 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... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.004s] 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 11/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] 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 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] 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 2/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [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... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building query seed array... [0.005s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6919,7 +6955,7 @@ Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6928,7 +6964,7 @@ 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... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] @@ -6942,48 +6978,48 @@ Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.001s] 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... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] 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 14/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] 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 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.003s] Building query seed array... [0.005s] 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 14/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.005s] 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... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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 15/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] @@ -6991,53 +7027,53 @@ 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... [0.005s] -Computing hash join... [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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.005s] 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 16/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.005s] 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 16/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] 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... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] 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 16/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.004s] +Computing alignments... Loading trace points... [0.005s] Sorting trace points... [0s] -Computing alignments... [0.631s] +Computing alignments... [0.677s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.637s] + [0.684s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7047,17 +7083,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.504s +Total time = 1.618s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -7065,12 +7101,12 @@ 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... [0.006s] +Masking reference... [0.008s] Initializing temporary storage... [0s] Building reference histograms... [0.026s] Allocating buffers... [0s] @@ -7086,59 +7122,59 @@ 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 1/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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... [0.003s] +Building reference seed array... [0.005s] 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 2/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] 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 2/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] 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 2/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] 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 2/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.005s] 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 3/16, index chunk 1/4. -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 3/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7159,28 +7195,28 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] 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 4/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] -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 4/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] 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 4/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7201,14 +7237,14 @@ 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... [0.005s] 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 5/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7229,49 +7265,49 @@ 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... [0.005s] 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 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.004s] 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 7/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 7/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] 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 7/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] 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 7/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.004s] 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 8/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7299,21 +7335,21 @@ 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... [0.002s] +Building reference seed array... [0.004s] 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 9/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 9/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7334,21 +7370,21 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.005s] 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 10/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.005s] 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 10/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7369,7 +7405,7 @@ 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... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7383,14 +7419,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] 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 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7418,14 +7454,14 @@ 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... [0.003s] +Building reference seed array... [0.005s] 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 13/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7439,28 +7475,28 @@ 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... [0.004s] +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 14/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] 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 14/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] 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 14/16, index chunk 4/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7474,42 +7510,42 @@ 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... [0.003s] +Building reference seed array... [0.005s] 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 15/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] 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 15/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] 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 16/16, index chunk 1/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.002s] 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 16/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.005s] 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 16/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.005s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7524,12 +7560,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0s] +Computing alignments... Loading trace points... [0.001s] Sorting trace points... [0s] Computing alignments... [0.005s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.006s] + [0.007s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7539,17 +7575,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.618s +Total time = 0.732s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -7557,9 +7593,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.014s] +Masking queries... [0.015s] Algorithm: Double-indexed -Building query histograms... [0.019s] +Building query histograms... [0.026s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -7568,35 +7604,35 @@ Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] 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... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] 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 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] 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... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] 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 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7617,14 +7653,14 @@ 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... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7638,49 +7674,49 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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 1/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] 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... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] 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... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.008s] 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 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7702,13 +7738,13 @@ Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. Building reference seed array... [0s] Building query seed array... [0.005s] -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 6/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7736,14 +7772,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7757,21 +7793,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] 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 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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 2/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7792,7 +7828,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7813,7 +7849,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7848,42 +7884,42 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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 2/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +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 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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... [0s] -Building query seed array... [0.006s] +Building query seed array... [0.005s] 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 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] 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 2/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7897,14 +7933,14 @@ 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... [0.005s] 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 1/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7918,7 +7954,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7932,7 +7968,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7953,21 +7989,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] 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 1/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.005s] 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 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -7981,7 +8017,7 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8002,14 +8038,14 @@ 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... [0.005s] +Building query seed array... [0.004s] 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 4/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -8031,17 +8067,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.601s +Total time = 0.769s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -8054,47 +8090,47 @@ Building query histograms... [0.012s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.006s] +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... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.012s] 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 reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.01s] +Searching alignments... [0.005s] 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... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, 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] @@ -8105,17 +8141,17 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] 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... [0.003s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, 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] @@ -8126,63 +8162,63 @@ Building query seed array... [0.002s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4. -Building reference seed array... [0.005s] +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... [0.003s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.008s] 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 reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.009s] 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... [0.007s] +Searching alignments... [0.009s] 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... [0.001s] -Computing hash join... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.009s] 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 query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.008s] 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 query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.009s] 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 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... [0.006s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.002s] @@ -8192,64 +8228,64 @@ Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, 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... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] 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 query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.004s] 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... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] 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 query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.008s] 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 query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.006s] Deallocating memory... [0s] 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... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.009s] 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... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.009s] 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... [0.001s] -Computing hash join... [0s] +Building query seed array... [0.002s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.008s] Deallocating memory... [0s] 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... [0.001s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] @@ -8259,61 +8295,61 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.001s] +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... [0.006s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. 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... [0.009s] Deallocating memory... [0s] @@ -8325,8 +8361,8 @@ Searching alignments... [0.008s] 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 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... [0.009s] @@ -8339,9 +8375,9 @@ Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, 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... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] Deallocating memory... [0s] @@ -8353,63 +8389,63 @@ Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, 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] Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.005s] -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... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.009s] 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 reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] 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 reference seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] 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 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... [0.008s] +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... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] 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 reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.004s] 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 reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -8417,45 +8453,45 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, 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... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0.001s] -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... [0.008s] 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 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... [0.009s] +Searching alignments... [0.007s] 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 reference seed array... [0.003s] Building query seed array... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. 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... [0.007s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +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... [0.002s] @@ -8466,38 +8502,38 @@ 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.006s] 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 query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, 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... [0.008s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. Building reference seed array... [0.002s] @@ -8510,10 +8546,10 @@ Clearing query masking... [0s] Computing alignments... Loading trace points... [0.005s] Sorting trace points... [0s] -Computing alignments... [0.226s] +Computing alignments... [0.238s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.232s] + [0.244s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8523,17 +8559,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.386s +Total time = 1.559s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -8541,67 +8577,67 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.024s] +Masking queries... [0.019s] Algorithm: Double-indexed Building query histograms... [0.012s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +Building reference histograms... [0.007s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.012s] 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... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.01s] 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... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] 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 query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] 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... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.009s] 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 query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] 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] -Computing hash join... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.003s] -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... [0.008s] @@ -8611,47 +8647,47 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query 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... [0.009s] +Searching alignments... [0.004s] 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... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, 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] -Searching alignments... [0.009s] +Searching alignments... [0.008s] 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 query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query 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... [0.009s] +Searching alignments... [0.007s] 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] -Computing hash join... [0.003s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] Deallocating memory... [0s] @@ -8660,31 +8696,31 @@ Building query seed array... [0.002s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] 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 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... [0.004s] +Searching alignments... [0.009s] 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 query seed array... [0.002s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] 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 query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, 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] @@ -8692,21 +8728,21 @@ 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 query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, 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] -Searching alignments... [0.005s] +Searching alignments... [0.009s] 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 query seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] @@ -8716,7 +8752,7 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -8728,48 +8764,48 @@ Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. 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... [0.009s] +Searching alignments... [0.008s] 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] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. -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] Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, 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] -Searching alignments... [0.008s] +Searching alignments... [0.009s] 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 query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] 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] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] 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... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] @@ -8777,14 +8813,14 @@ Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. 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... [0.009s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4. -Building reference seed array... [0.002s] +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... [0.007s] Deallocating memory... [0s] @@ -8793,19 +8829,19 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.012s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. 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... [0.009s] Deallocating memory... [0s] @@ -8821,40 +8857,40 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] 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... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.009s] 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 query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] 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] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. Building reference seed array... [0.002s] -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... [0.008s] Deallocating memory... [0s] @@ -8863,11 +8899,11 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, 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... [0.009s] @@ -8889,7 +8925,7 @@ Processing query block 1, reference block 1/1, shape 13/16, 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... [0.009s] Deallocating memory... [0s] @@ -8898,11 +8934,11 @@ Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.008s] 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 query seed array... [0.003s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.008s] @@ -8910,102 +8946,102 @@ Processing query block 1, reference block 1/1, shape 13/16, 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... [0.009s] +Searching alignments... [0.008s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, 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... [0.003s] +Searching alignments... [0.008s] 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] -Computing hash join... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] 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 query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] 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 reference seed array... [0.002s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, 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... [0.008s] +Searching alignments... [0.009s] 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] -Computing hash join... [0.001s] -Masking low complexity seeds... [0.002s] -Searching alignments... [0.012s] +Building query seed array... [0.002s] +Computing hash join... [0s] +Masking low complexity seeds... [0s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. -Building reference seed array... [0.008s] -Building query seed array... [0.001s] -Computing hash join... [0.007s] -Masking low complexity seeds... [0.004s] -Searching alignments... [0.013s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] +Computing hash join... [0s] +Masking low complexity seeds... [0s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4. -Building reference seed array... [0.015s] -Building query seed array... [0.006s] -Computing hash join... [0.008s] -Masking low complexity seeds... [0.007s] -Searching alignments... [0.008s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.011s] +Searching alignments... [0.02s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.015s] -Building query seed array... [0.023s] +Building reference seed array... [0.025s] +Building query seed array... [0.004s] Computing hash join... [0.007s] -Masking low complexity seeds... [0.003s] -Searching alignments... [0.005s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.016s] -Building query seed array... [0.019s] -Computing hash join... [0.015s] -Masking low complexity seeds... [0.003s] -Searching alignments... [0.013s] +Building reference seed array... [0s] +Building query seed array... [0.003s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4. -Building reference seed array... [0.018s] -Building query seed array... [0.019s] +Building reference seed array... [0.005s] +Building query seed array... [0.012s] Computing hash join... [0.003s] Masking low complexity seeds... [0.003s] -Searching alignments... [0.005s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -Building reference seed array... [0.011s] -Building query seed array... [0.023s] -Computing hash join... [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... [0.008s] +Searching alignments... [0.004s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.012s] +Computing alignments... Loading trace points... [0.004s] Sorting trace points... [0s] -Computing alignments... [0.2s] +Computing alignments... [0.196s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.214s] + [0.201s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9015,17 +9051,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.719s +Total time = 1.532s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -9035,60 +9071,60 @@ Loading query sequences... [0s] Masking queries... [0s] Algorithm: Double-indexed -Building query histograms... [0.012s] +Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.001s] +Masking reference... [0.004s] Initializing temporary storage... [0s] -Building reference histograms... [0.004s] +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... [0.001s] +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 2/4. -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] 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... [0.023s] -Computing hash join... [0.012s] -Masking low complexity seeds... [0.002s] -Searching alignments... [0.007s] +Building reference seed array... [0.002s] +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... [0.019s] -Building query seed array... [0.007s] -Computing hash join... [0.003s] -Masking low complexity seeds... [0.011s] -Searching alignments... [0.011s] +Building reference seed array... [0.002s] +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 2/16, index chunk 1/4. -Building reference seed array... [0.016s] -Building query seed array... [0.023s] -Computing hash join... [0.007s] -Masking low complexity seeds... [0.007s] -Searching alignments... [0.007s] +Building reference seed array... [0.002s] +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 2/16, index chunk 2/4. -Building reference seed array... [0.019s] -Building query seed array... [0.02s] -Computing hash join... [0.003s] -Masking low complexity seeds... [0.015s] -Searching alignments... [0.019s] +Building reference seed array... [0.002s] +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 2/16, index chunk 3/4. -Building reference seed array... [0.015s] -Building query seed array... [0.015s] -Computing hash join... [0.011s] -Masking low complexity seeds... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. @@ -9099,214 +9135,214 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. -Building reference seed array... [0s] +Building reference seed array... [0.001s] 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 3/16, index chunk 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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 3/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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 3/16, index chunk 4/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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 4/16, index chunk 1/4. -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] 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 reference seed array... [0.002s] 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 4/16, index chunk 3/4. -Building reference seed array... [0s] +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 4/16, index chunk 4/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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 5/16, index chunk 1/4. -Building reference seed array... [0s] +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 5/16, index chunk 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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 5/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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 5/16, index chunk 4/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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 1/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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... [0s] +Building reference seed array... [0.002s] 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 4/4. -Building reference seed array... [0.007s] -Building query seed array... [0.01s] +Building reference seed array... [0.002s] +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 7/16, index chunk 1/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] 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 7/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.004s] -Computing hash join... [0.003s] -Masking low complexity seeds... [0.011s] -Searching alignments... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.011s] +Building reference seed array... [0.002s] Building query seed array... [0s] 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 7/16, index chunk 4/4. -Building reference seed array... [0.012s] -Building query seed array... [0.006s] -Computing hash join... [0.002s] -Masking low complexity seeds... [0.005s] -Searching alignments... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.022s] -Computing hash join... [0.007s] -Masking low complexity seeds... [0.003s] -Searching alignments... [0.015s] +Building reference seed array... [0.002s] +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 8/16, index chunk 2/4. -Building reference seed array... [0.011s] -Building query seed array... [0.008s] -Computing hash join... [0.005s] +Building reference seed array... [0.002s] +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 8/16, 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] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.007s] -Computing hash join... [0.003s] -Masking low complexity seeds... [0.003s] -Searching alignments... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.002s] 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 9/16, index chunk 2/4. -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] 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... [0.004s] +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 9/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] -Computing hash join... [0.002s] -Masking low complexity seeds... [0.002s] -Searching alignments... [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 10/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0.001s] -Searching alignments... [0.006s] +Masking low complexity seeds... [0s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -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] -Searching alignments... [0.002s] +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] @@ -9316,123 +9352,123 @@ 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... [0.004s] +Building reference seed array... [0.002s] 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 11/16, index chunk 1/4. -Building reference seed array... [0.007s] +Building reference seed array... [0.002s] 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 11/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.004s] +Building reference seed array... [0.002s] +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 11/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +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 11/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.006s] +Building reference seed array... [0.002s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.013s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.008s] -Building query 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... [0.005s] +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 reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0.01s] +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... [0.013s] -Building query seed array... [0.009s] +Building reference seed array... [0.002s] +Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0.003s] -Searching alignments... [0.01s] +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... [0.007s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0.001s] -Searching alignments... [0.012s] +Masking low complexity seeds... [0s] +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... [0.007s] -Building query seed array... [0.015s] -Computing hash join... [0.004s] -Masking low complexity seeds... [0.003s] -Searching alignments... [0.005s] +Building reference seed array... [0.002s] +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 13/16, index chunk 2/4. -Building reference seed array... [0.007s] -Building query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0.003s] +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... [0.011s] -Computing hash join... [0.004s] +Building reference seed array... [0.002s] +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 13/16, index chunk 4/4. -Building reference seed array... [0.012s] -Building query seed array... [0.007s] +Building reference seed array... [0.002s] +Building query seed array... [0s] 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 14/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.011s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0.004s] +Masking low complexity seeds... [0s] 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... [0.006s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0.008s] +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... [0.015s] +Building reference seed array... [0.002s] Building query seed array... [0s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0s] 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... [0.011s] -Computing hash join... [0.007s] -Masking low complexity seeds... [0.007s] -Searching alignments... [0.001s] +Building reference seed array... [0.002s] +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 15/16, index chunk 1/4. Building reference seed array... [0.002s] @@ -9442,49 +9478,49 @@ 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... [0s] +Building reference seed array... [0.002s] 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 15/16, index chunk 3/4. -Building reference seed array... [0.01s] -Building query seed array... [0.007s] -Computing hash join... [0.008s] -Masking low complexity seeds... [0.003s] -Searching alignments... [0.001s] +Building reference seed array... [0.002s] +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 15/16, index chunk 4/4. -Building reference seed array... [0.007s] -Building query seed array... [0.004s] -Computing hash join... [0.007s] +Building reference seed array... [0.003s] +Building query seed array... [0s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +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... [0.001s] -Building query seed array... [0.006s] +Building reference seed array... [0.002s] +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 16/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +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 16/16, 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] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. -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] @@ -9492,12 +9528,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0s] +Computing alignments... Loading trace points... [0.001s] Sorting trace points... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.004s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.004s] + [0.005s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9507,17 +9543,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.112s +Total time = 0.572s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -9525,9 +9561,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.018s] +Masking queries... [0.025s] Algorithm: Double-indexed -Building query histograms... [0.007s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -9536,112 +9572,112 @@ Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. 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] +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... [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] 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... [0.001s] +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 1/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0s] -Computing hash join... [0.007s] +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 2/16, index chunk 1/4. -Building reference seed array... [0.001s] +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 2/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +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 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] 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... [0.005s] +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 3/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0s] Building query seed array... [0.001s] -Computing hash join... [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 3/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0s] 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 3/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +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 3/16, index chunk 4/4. 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... [0.008s] +Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, 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] 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... [0s] +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... [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] @@ -9649,22 +9685,22 @@ Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. 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] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +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... [0.001s] -Computing hash join... [0.008s] -Masking low complexity seeds... [0.001s] +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 4/4. @@ -9676,48 +9712,48 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0s] +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 2/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 6/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0s] +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 6/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0.006s] -Searching alignments... [0.007s] +Masking low complexity seeds... [0s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0s] +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 7/16, index chunk 2/4. Building reference seed array... [0s] -Building query 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 7/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9732,13 +9768,13 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] -Computing hash join... [0.007s] +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 8/16, index chunk 2/4. -Building reference seed array... [0.004s] +Building reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9746,70 +9782,70 @@ 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... [0s] +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 8/16, index chunk 4/4. 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 9/16, index chunk 1/4. 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... [0.006s] -Searching alignments... [0.007s] +Masking low complexity seeds... [0s] +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... [0.007s] -Building query seed array... [0.007s] -Computing hash join... [0.003s] -Masking low complexity seeds... [0.003s] -Searching alignments... [0.003s] +Building reference seed array... [0s] +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 9/16, index chunk 3/4. -Building reference seed array... [0.007s] -Building query seed array... [0.012s] +Building reference seed array... [0s] +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 9/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +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 10/16, index chunk 2/4. 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] 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... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +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... [0s] -Building query seed array... [0.008s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9819,12 +9855,12 @@ 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 2/4. -Building reference seed array... [0.001s] +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] @@ -9836,7 +9872,7 @@ 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... [0.006s] +Building reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9851,38 +9887,38 @@ 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... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0.012s] +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... [0.006s] +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 12/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +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 1/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.001s] +Building reference seed array... [0s] +Building query seed array... [0.002s] 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 13/16, index chunk 3/4. Building reference seed array... [0s] @@ -9893,36 +9929,36 @@ Deallocating memory... [0s] 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] +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 1/4. 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... [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 14/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0.003s] -Searching alignments... [0.001s] +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... [0.006s] +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 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] -Computing hash join... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -9935,35 +9971,35 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. 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... [0.007s] +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... [0s] +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 15/16, index chunk 4/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. 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] 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... [0.013s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9973,23 +10009,23 @@ 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 16/16, index chunk 4/4. 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... [0.006s] +Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] Computing alignments... Loading trace points... [0.001s] Sorting trace points... [0s] -Computing alignments... [0.002s] +Computing alignments... [0.004s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.004s] + [0.007s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9999,17 +10035,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.59s +Total time = 0.468s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -10022,12 +10058,12 @@ Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.001s] +Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.007s] +Building reference histograms... [0.008s] 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 reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10048,18 +10084,18 @@ 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] +Building reference seed array... [0.002s] 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 2/16, index chunk 1/4. -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] -Searching alignments... [0.002s] +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] @@ -10069,14 +10105,14 @@ 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 query seed array... [0.007s] +Building reference seed array... [0.002s] +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 2/16, index chunk 4/4. -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] @@ -10090,56 +10126,56 @@ Searching alignments... [0s] 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 reference seed array... [0.002s] Building query seed array... [0s] -Computing hash join... [0.006s] +Computing hash join... [0s] Masking low complexity seeds... [0s] 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 query seed array... [0.001s] +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 3/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +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 4/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0.01s] +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 4/16, index chunk 2/4. -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] 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 reference seed array... [0.002s] 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 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] 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... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10160,18 +10196,18 @@ 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... [0.001s] +Building reference seed array... [0.002s] 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 1/4. -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] -Searching alignments... [0.001s] +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... [0.001s] @@ -10181,21 +10217,21 @@ 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... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +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 4/4. -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] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10203,14 +10239,14 @@ 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... [0s] +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 7/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10218,34 +10254,34 @@ 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... [0s] -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 8/16, index chunk 1/4. -Building reference seed array... [0.01s] +Building reference seed array... [0.001s] 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 8/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.002s] Building query seed array... [0s] -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 8/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.002s] +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 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10258,21 +10294,21 @@ 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... [0.001s] +Building reference seed array... [0.002s] 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 9/16, 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] 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] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10286,7 +10322,7 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4. -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] @@ -10307,7 +10343,7 @@ 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... [0.001s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10328,7 +10364,7 @@ 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 reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10350,7 +10386,7 @@ 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... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10370,14 +10406,14 @@ 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... [0.001s] 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 13/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10391,14 +10427,14 @@ 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... [0.003s] +Building reference seed array... [0.001s] 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 14/16, index chunk 2/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10420,27 +10456,27 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.001s] +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 15/16, index chunk 2/4. -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] 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... [0.001s] 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 15/16, 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] @@ -10476,12 +10512,12 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0s] +Computing alignments... Loading trace points... [0.001s] Sorting trace points... [0s] Computing alignments... [0.003s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.006s] + [0.005s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10491,17 +10527,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.455s +Total time = 0.396s 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.td2dDWEXlJ/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.wSZbnPk58M/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.td2dDWEXlJ +Temporary directory: /tmp/tmp.wSZbnPk58M #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -10509,9 +10545,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.018s] +Masking queries... [0.02s] Algorithm: Double-indexed -Building query histograms... [0.011s] +Building query histograms... [0.006s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -10527,35 +10563,35 @@ 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... [0.002s] +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 1/16, index chunk 3/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10584,40 +10620,40 @@ Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. Building reference seed array... [0s] Building query seed array... [0.001s] -Computing hash join... [0.004s] +Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, 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] 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 reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10625,14 +10661,14 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.003s] -Computing hash join... [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 5/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10646,21 +10682,21 @@ 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +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 6/16, index chunk 1/4. 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] @@ -10681,21 +10717,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +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 7/16, 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] @@ -10709,56 +10745,56 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.003s] -Computing hash join... [0.008s] +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 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] 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... [0.002s] +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 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.001s] +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 9/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +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 9/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0s] +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 9/16, index chunk 3/4. 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] @@ -10772,21 +10808,21 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. 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] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. 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] @@ -10807,28 +10843,28 @@ 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... [0.001s] 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 3/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. 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] @@ -10842,138 +10878,138 @@ 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4. 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] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +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 14/16, index chunk 1/4. 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] 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4. 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] +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] -Building query seed array... [0.002s] +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 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] 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... [0.002s] +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 4/4. Building reference seed array... [0s] -Building query 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 16/16, index chunk 1/4. Building reference seed array... [0s] -Building query 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 16/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.001s] +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 16/16, index chunk 3/4. 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4. Building reference seed array... [0s] -Building query 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] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... Loading trace points... [0.001s] +Computing alignments... Loading trace points... [0s] Sorting trace points... [0s] -Computing alignments... [0.006s] +Computing alignments... [0.002s] Deallocating buffers... [0s] Loading trace points... [0s] - [0.008s] + [0.004s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10983,10 +11019,10 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.593s +Total time = 0.37s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ rm -rf /tmp/tmp.td2dDWEXlJ ++ rm -rf /tmp/tmp.wSZbnPk58M make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.9' create-stamp debian/debhelper-build-stamp dh_prep @@ -11027,8 +11063,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'diamond-aligner' in '../diamond-aligner_2.1.9-1_arm64.deb'. dpkg-deb: building package 'diamond-aligner-dbgsym' in '../diamond-aligner-dbgsym_2.1.9-1_arm64.deb'. +dpkg-deb: building package 'diamond-aligner' in '../diamond-aligner_2.1.9-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../diamond-aligner_2.1.9-1_arm64.buildinfo dpkg-genchanges --build=binary -O../diamond-aligner_2.1.9-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -11036,12 +11072,14 @@ 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/233616/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/233616/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/1541781 and its subdirectories -I: Current time: Tue Jan 7 04:17:40 -12 2025 -I: pbuilder-time-stamp: 1736266660 +I: removing directory /srv/workspace/pbuilder/233616 and its subdirectories +I: Current time: Tue Feb 10 12:45:48 +14 2026 +I: pbuilder-time-stamp: 1770677148