Diff of the two buildlogs: -- --- b1/build.log 2025-10-21 01:38:27.178543177 +0000 +++ b2/build.log 2025-10-21 01:47:08.887231407 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Oct 20 13:33:58 -12 2025 -I: pbuilder-time-stamp: 1761010438 +I: Current time: Mon Nov 23 22:01:29 +14 2026 +I: pbuilder-time-stamp: 1795420889 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -22,53 +22,85 @@ dpkg-source: info: unpacking diamond-aligner_2.1.14-1.debian.tar.xz I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/1342373/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/2242308/tmp/hooks/D01_modify_environment starting +debug: Running on codethink03-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 Nov 23 08:01 /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/2242308/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/2242308/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]="3" [2]="3" [3]="1" [4]="release" [5]="aarch64-unknown-linux-gnu") + BASH_VERSION='5.3.3(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='unstable' - HOME='/root' - HOST_ARCH='arm64' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=aarch64 + HOST_ARCH=arm64 IFS=' ' - INVOCATION_ID='f4089107d17548c99009aec72e1f317d' - 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='1342373' - PS1='# ' - PS2='> ' + INVOCATION_ID=a65e4fbb82d34d1685c753c5ec48e8cc + 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=2242308 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.Fzw1Ps1c/pbuilderrc_hDqX --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Fzw1Ps1c/b1 --logfile b1/build.log diamond-aligner_2.1.14-1.dsc' - SUDO_GID='109' - SUDO_HOME='/var/lib/jenkins' - 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.Fzw1Ps1c/pbuilderrc_C4P0 --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Fzw1Ps1c/b2 --logfile b2/build.log diamond-aligner_2.1.14-1.dsc' + SUDO_GID=109 + SUDO_HOME=/var/lib/jenkins + 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 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux + Linux i-capture-the-hostname 6.12.48+deb13-cloud-arm64 #1 SMP Debian 6.12.48-1 (2025-09-20) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/1342373/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/2242308/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -170,7 +202,7 @@ Get: 60 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.28 [941 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB] -Fetched 30.1 MB in 0s (154 MB/s) +Fetched 30.1 MB in 0s (66.3 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1: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 ... 19960 files and directories currently installed.) @@ -433,7 +465,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/diamond-aligner-2.1.14/ && 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_2.1.14-1_source.changes +I: user script /srv/workspace/pbuilder/2242308/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/2242308/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/diamond-aligner-2.1.14/ && 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_2.1.14-1_source.changes dpkg-buildpackage: info: source package diamond-aligner dpkg-buildpackage: info: source version 2.1.14-1 dpkg-buildpackage: info: source distribution unstable @@ -494,8 +530,8 @@ -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE --- Configuring done (2.7s) --- Generating done (0.1s) +-- Configuring done (3.3s) +-- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -525,35 +561,35 @@ make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu' cd /build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/diamond-aligner-2.1.14 /build/reproducible-path/diamond-aligner-2.1.14 /build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu /build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu/CMakeFiles/arch_neon.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu' -make -f CMakeFiles/arch_neon.dir/build.make CMakeFiles/arch_neon.dir/build -make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu' make -f CMakeFiles/arch_generic.dir/build.make CMakeFiles/arch_generic.dir/build make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu' +make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu' +make -f CMakeFiles/arch_neon.dir/build.make CMakeFiles/arch_neon.dir/build make[3]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu' -[ 1%] Building CXX object CMakeFiles/arch_generic.dir/src/search/stage1_2.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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o -MF CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o.d -o CMakeFiles/arch_generic.dir/src/search/stage1_2.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/search/stage1_2.cpp -[ 2%] Building CXX object CMakeFiles/arch_neon.dir/src/tools/benchmark.cpp.o -[ 3%] Building CXX object CMakeFiles/arch_neon.dir/src/search/stage1_2.cpp.o -[ 3%] Building CXX object CMakeFiles/arch_neon.dir/src/dp/swipe/swipe_wrapper.cpp.o -[ 4%] Building CXX object CMakeFiles/arch_neon.dir/src/dp/scan_diags.cpp.o -[ 4%] Building CXX object CMakeFiles/arch_neon.dir/src/masking/tantan.cpp.o -[ 4%] Building CXX object CMakeFiles/arch_neon.dir/src/dp/swipe/banded_3frame_swipe.cpp.o -[ 4%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/banded_3frame_swipe.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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -DDISPATCH_ARCH=ARCH_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/search/stage1_2.cpp.o -MF 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-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++20 -DDISPATCH_ARCH=ARCH_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/dp/swipe/swipe_wrapper.cpp.o -MF CMakeFiles/arch_neon.dir/src/dp/swipe/swipe_wrapper.cpp.o.d -o CMakeFiles/arch_neon.dir/src/dp/swipe/swipe_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/swipe_wrapper.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:369, from /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:27: /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_NEON::PlainObjectBase::_check_template_params() [with Derived = Eigen_NEON::Array]’: @@ -620,6 +656,8 @@ 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/build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:741:37: required from ‘void Eigen_NEON::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen_NEON::Array; SrcXprType = Eigen_NEON::Array; Functor = mul_assign_op]’ @@ -793,15 +831,6 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_NEON::Array::’ and ‘Eigen_NEON::internal::unpacket_traits<__Float32x4_t>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -[ 7%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/swipe/swipe_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-2.1.14/src 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diagnostics -[ 8%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/scan_diags.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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/scan_diags.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/scan_diags.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/scan_diags.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/scan_diags.cpp -[ 9%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o -/usr/bin/c++ -DLEFTMOST_SEED_FILTER -DMAX_SHAPE_LEN=19 -DSEQ_MASK -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/ungapped_simd.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/ungapped_simd.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:369, from /build/reproducible-path/diamond-aligner-2.1.14/src/masking/tantan.cpp:27: /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/PlainObjectBase.h: In instantiation of ‘static void Eigen_GENERIC::PlainObjectBase::_check_template_params() [with Derived = Eigen_GENERIC::Array]’: @@ -1041,11 +1070,18 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/AssignEvaluator.h:432:31: warning: arithmetic between different enumeration types ‘Eigen_GENERIC::Array::’ and ‘Eigen_GENERIC::internal::unpacket_traits<__Float32x4_t>::’ is deprecated [-Wdeprecated-enum-enum-conversion] 432 | alignedSize = (size/packetSize)*packetSize }; | ~~~~~^~~~~~~~~~~~ -[ 9%] 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 -DSTRICT_BAND -DWITH_NEON -D_ITERATOR_DEBUG_LEVEL=0 -I/build/reproducible-path/diamond-aligner-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o -MF CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o.d -o CMakeFiles/arch_generic.dir/src/dp/swipe/anchored_wrapper.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/anchored_wrapper.cpp -[ 10%] Building CXX object CMakeFiles/arch_generic.dir/src/dp/score_profile.cpp.o +[ 8%] 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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -DDISPATCH_ARCH=ARCH_GENERIC -DARCH_ID=0 -DEigen=Eigen_GENERIC -MD -MT 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-Wno-unused-variable -Wno-uninitialized -Wno-deprecated-copy -Wno-unknown-warning-option -O3 -DNDEBUG -std=gnu++20 -DDISPATCH_ARCH=ARCH_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/dp/scan_diags.cpp.o -MF CMakeFiles/arch_neon.dir/src/dp/scan_diags.cpp.o.d -o CMakeFiles/arch_neon.dir/src/dp/scan_diags.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/scan_diags.cpp +cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics +[ 9%] Building CXX object CMakeFiles/arch_neon.dir/src/dp/ungapped_simd.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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -DDISPATCH_ARCH=ARCH_NEON -DARCH_ID=4 -D__ARM_NEON -D__aarch64__ -DEigen=Eigen_NEON -MD -MT CMakeFiles/arch_neon.dir/src/dp/ungapped_simd.cpp.o -MF CMakeFiles/arch_neon.dir/src/dp/ungapped_simd.cpp.o.d -o CMakeFiles/arch_neon.dir/src/dp/ungapped_simd.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/dp/ungapped_simd.cpp +[ 10%] Building CXX object 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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -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-2.1.14/src/dp/swipe/anchored_wrapper.cpp +[ 10%] 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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -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-2.1.14/src/dp/score_profile.cpp In file included from /usr/include/c++/15/list:64, from /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/swipe_wrapper.cpp:22: In function ‘constexpr void std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, @@ -1085,8 +1121,8 @@ In function ‘constexpr void std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, inlined from ‘constexpr void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/15/bits/stl_algobase.h:979:21, inlined from ‘constexpr void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/15/bits/stl_algobase.h:1011:20, - inlined from ‘DP::Swipe::ARCH_NEON::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_matrix.h:66:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_swipe.h:165:9: + inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_matrix.h:66:12, + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_swipe.h:165:9: /usr/include/c++/15/bits/stl_algobase.h:925:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 925 | *__first = __val; | ~~~~~~~~~^~~~~~~ @@ -1094,7 +1130,7 @@ inlined from ‘constexpr void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/15/bits/stl_algobase.h:979:21, inlined from ‘constexpr void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/15/bits/stl_algobase.h:1011:20, inlined from ‘DP::Swipe::ARCH_NEON::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_matrix.h:66:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_swipe.h:165:9: + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_swipe.h:165:9: /usr/include/c++/15/bits/stl_algobase.h:925:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 925 | *__first = __val; | ~~~~~~~~~^~~~~~~ @@ -1102,15 +1138,15 @@ inlined from ‘constexpr void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/15/bits/stl_algobase.h:979:21, inlined from ‘constexpr void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/15/bits/stl_algobase.h:1011:20, inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_matrix.h:66:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_swipe.h:165:9: + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_swipe.h:165:9: /usr/include/c++/15/bits/stl_algobase.h:925:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 925 | *__first = __val; | ~~~~~~~~~^~~~~~~ In function ‘constexpr void std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’, inlined from ‘constexpr void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = int*; _Tp = int]’ at /usr/include/c++/15/bits/stl_algobase.h:979:21, inlined from ‘constexpr void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = int*; _Tp = int]’ at /usr/include/c++/15/bits/stl_algobase.h:1011:20, - inlined from ‘DP::Swipe::ARCH_GENERIC::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_matrix.h:66:12, - inlined from ‘std::__cxx11::list DP::Swipe::ARCH_GENERIC::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_swipe.h:165:9: + inlined from ‘DP::Swipe::ARCH_NEON::Matrix::Matrix(int, int) [with Sv = int]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_matrix.h:66:12, + inlined from ‘std::__cxx11::list DP::Swipe::ARCH_NEON::swipe(It, It, std::atomic*, Cbs, DP::TargetVec&, DP::Params&) [with Sv = int; Cbs = DP::NoCBS; It = StringSetBase::ConstIterator; Cfg = SwipeConfig, int, DummyIdMask >]’ at /build/reproducible-path/diamond-aligner-2.1.14/src/dp/swipe/full_swipe.h:165:9: /usr/include/c++/15/bits/stl_algobase.h:925:18: warning: ‘void* __builtin_memset(void*, int, long unsigned int)’ specified bound 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=] 925 | *__first = __val; | ~~~~~~~~~^~~~~~~ @@ -2749,39 +2785,39 @@ At global scope: cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu' -[ 10%] Built target arch_neon -make[3]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu' [ 10%] Built target arch_generic +make[3]: Leaving directory 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-I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -MD -MT CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o -MF CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/stats/blast/ncbi.cpp +[ 99%] Building CXX object CMakeFiles/diamond.dir/src/search/hit_buffer.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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -MD -MT CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -MF CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o.d -o CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/search/hit_buffer.cpp In file included from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Core:369, from /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/Dense:1, from /build/reproducible-path/diamond-aligner-2.1.14/src/util/algo/mcl.cpp:1: @@ -3302,10 +3342,6 @@ /build/reproducible-path/diamond-aligner-2.1.14/src/lib/Eigen/src/Core/CoreEvaluators.h:681:51: warning: arithmetic between different enumeration types ‘Eigen::internal::unary_evaluator, 1, -1, false> >, Eigen::internal::IndexBased, double>::’ and ‘Eigen::internal::evaluator, -1, 1, true> >::’ is deprecated [-Wdeprecated-enum-enum-conversion] 681 | CoeffReadCost = evaluator::CoeffReadCost + evaluator::CoeffReadCost + functor_traits::Cost, | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object CMakeFiles/diamond.dir/src/stats/blast/ncbi.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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -MD -MT CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o -MF CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o.d -o CMakeFiles/diamond.dir/src/stats/blast/ncbi.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/stats/blast/ncbi.cpp -[ 99%] Building CXX object CMakeFiles/diamond.dir/src/search/hit_buffer.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-2.1.14/src -I/build/reproducible-path/diamond-aligner-2.1.14/src/lib -g -O2 -ffile-prefix-map=/build/reproducible-path/diamond-aligner-2.1.14=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -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++20 -MD -MT CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -MF CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o.d -o CMakeFiles/diamond.dir/src/search/hit_buffer.cpp.o -c /build/reproducible-path/diamond-aligner-2.1.14/src/search/hit_buffer.cpp cc1plus: note: unrecognized command-line option ‘-Wno-unknown-warning-option’ may have been intended to silence earlier diagnostics [100%] Linking CXX executable diamond /usr/bin/cmake -E cmake_link_script CMakeFiles/diamond.dir/link.txt --verbose=1 @@ -3317,17 +3353,17 @@ make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu' debian/rules override_dh_auto_test make[1]: Entering directory '/build/reproducible-path/diamond-aligner-2.1.14' -cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games sh diamond-calls -+ mktemp -d -+ TESTDIR=/tmp/tmp.6OycLsGn47 -+ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.6OycLsGn47/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive +cd debian/tests && PATH=/build/reproducible-path/diamond-aligner-2.1.14/obj-aarch64-linux-gnu:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path sh diamond-calls +++ mktemp -d ++ TESTDIR=/tmp/tmp.M86lnC5iOP ++ diamond blastp --threads 1 --db test/C.faa.diamond --query test/E.faa --out /tmp/tmp.M86lnC5iOP/E.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -3335,466 +3371,466 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.007s] +Masking queries... [0.003s] Algorithm: Double-indexed -Building query histograms... [0.027s] +Building query histograms... [0.018s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.007s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.023s] +Building reference histograms... [0.021s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.006s] +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... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] +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... [0.005s] -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... [0.002s] 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] +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 1/4. -Building reference seed array... [0.004s] -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... [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... [0.005s] +Building reference seed array... [0.002s] 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 2/16, index chunk 3/4. -Building reference seed array... [0.004s] -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... [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... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [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 3/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +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 2/4. Building reference seed array... [0.003s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +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 3/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.004s] +Building reference seed array... [0.005s] +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... [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... [0.004s] 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... [0.005s] +Building reference seed array... [0.006s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] +Computing hash join... [0s] +Masking low complexity seeds... [0.001s] +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... [0.003s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.004s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.003s] 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... [0.005s] -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 5/16, index chunk 1/4. -Building reference seed array... [0.004s] -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] +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... [0.004s] -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] +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... [0.005s] -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 5/16, index chunk 4/4. Building reference seed array... [0.005s] -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... [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... [0.005s] -Building query seed array... [0.005s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] 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 6/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.003s] +Building reference seed array... [0.003s] +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 6/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +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 6/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 7/16, index chunk 1/4. -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 7/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] 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 7/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.008s] +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 7/16, index chunk 4/4. -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... [0.006s] +Computing hash join... [0.006s] 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 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 8/16, index chunk 2/4. -Building reference seed array... [0.003s] -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] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] -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] +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... [0.003s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.002s] +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 9/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.006s] +Building query seed array... [0.005s] +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 9/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.001s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. Building reference seed array... [0.003s] Building query seed array... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.006s] 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... [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] 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] +Building reference seed array... [0.008s] +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... [0.003s] -Building query seed array... [0.005s] -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] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.003s] +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 10/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] +Computing hash join... [0.004s] 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... [0.003s] -Building query seed array... [0.001s] -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 11/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] +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 11/16, 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... [0.004s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.004s] 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 12/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.013s] +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... [0.001s] -Building query seed array... [0.003s] +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 12/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] +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 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] +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... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, 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... [0.001s] +Computing hash join... [0.004s] 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 2/4. -Building reference seed array... [0.003s] -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... [0.002s] 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... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.008s] +Computing hash join... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.006s] 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... [0.004s] +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... [0.001s] 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... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.009s] +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 14/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.004s] +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 14/16, 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... [0.009s] +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... [0.003s] +Building reference seed array... [0.002s] +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 15/16, 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... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.003s] 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 query seed array... [0.003s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 15/16, 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... [0s] +Searching alignments... [0.007s] 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... [0.005s] -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 16/16, 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... [0.001s] +Computing hash join... [0.002s] 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... [0.003s] -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... [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... [0.003s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.003s] -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... [0.002s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.451s] +Computing alignments... [0.391s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -3804,484 +3840,484 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.384s +Total time = 1.305s 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.6OycLsGn47/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.M86lnC5iOP/C.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) Block size = 2000000000 Opening the input file... [0s] Opening the output file... [0s] -Loading query sequences... [0.001s] -Masking queries... [0.007s] +Loading query sequences... [0.005s] +Masking queries... [0.003s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.018s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.007s] +Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.011s] +Building reference histograms... [0.019s] 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... [0.005s] -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 1/16, index chunk 2/4. -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... [0.002s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.002s] +Computing hash join... [0s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.003s] 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... [0.001s] Building query seed array... [0.005s] -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 2/16, 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... [0.007s] +Building query seed array... [0.002s] +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 2/16, index chunk 2/4. Building reference seed array... [0.005s] -Building query seed array... [0.005s] -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 2/16, index chunk 3/4. -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] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.004s] 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... [0.004s] +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 3/16, 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... [0.007s] +Building query seed array... [0.007s] +Computing hash join... [0.004s] 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... [0.003s] -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 3/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] +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 3/16, 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... [0.001s] +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 4/16, index chunk 1/4. -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 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... [0.007s] +Building query seed array... [0.007s] +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 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] +Building reference 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 4/16, 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... [0.001s] +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... [0.005s] -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... [0.005s] 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... [0.005s] -Building query seed array... [0.003s] -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... [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 reference seed array... [0.001s] Building query seed array... [0.003s] -Computing hash join... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.003s] -Computing hash join... [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... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.013s] +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... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building query seed array... [0.004s] +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 6/16, index chunk 3/4. -Building reference seed array... [0.003s] -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] +Masking low complexity seeds... [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... [0.003s] -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... [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 query seed array... [0.006s] 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 7/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] 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... [0.004s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +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... [0.005s] -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 8/16, 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 8/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] +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 3/4. -Building reference seed array... [0.005s] -Building query 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... [0.005s] -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... [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... [0.005s] +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 9/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] +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 9/16, 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... [0.006s] +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 9/16, 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... [0.003s] +Building query seed array... [0.001s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] -Deallocating memory... [0s] +Deallocating memory... [0.001s] 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... [0.004s] -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] +Searching alignments... [0.003s] 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 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... [0s] +Searching alignments... [0.002s] 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 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 10/16, index chunk 4/4. -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... [0.002s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.003s] 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... [0.001s] +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 11/16, 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... [0.009s] +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 11/16, index chunk 3/4. Building reference seed array... [0.005s] -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 11/16, index chunk 4/4. -Building reference seed array... [0.005s] -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 12/16, index chunk 1/4. -Building reference seed array... [0.005s] -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 12/16, index chunk 2/4. -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... [0.002s] +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 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... [0s] +Searching alignments... [0.001s] 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... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.001s] +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 13/16, 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... [0.003s] +Building query seed array... [0.002s] +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 13/16, 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... [0.004s] +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 3/4. -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] 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... [0.005s] -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... [0.005s] 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... [0.008s] +Building query seed array... [0.003s] +Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] -Deallocating memory... [0s] +Searching alignments... [0.001s] +Deallocating memory... [0.003s] 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] +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 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.005s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, 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... [0.002s] +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 1/4. Building reference seed array... [0.004s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +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 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... [0.008s] +Computing hash join... [0.009s] 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... [0.005s] -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] +Searching alignments... [0.007s] 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... [0.005s] -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 16/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.012s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.001s] +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... [0.005s] -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... [0.001s] 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... [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... [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... [0.008s] +Building query seed array... [0.005s] +Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.098s] +Computing alignments... [0.076s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4291,17 +4327,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.091s +Total time = 0.954s 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.6OycLsGn47/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.M86lnC5iOP/L.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -4309,137 +4345,137 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.004s] +Masking queries... [0.002s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.007s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.007s] +Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.025s] +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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.001s] +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... [0.004s] -Building query 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 1/16, 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... [0.003s] 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... [0.004s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.003s] 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... [0.001s] +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... [0.001s] +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 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] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.004s] -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 3/16, 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] 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... [0.002s] +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 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.002s] 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... [0.005s] -Building query 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] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +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... [0.004s] -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 4/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.004s] 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] +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... [0.003s] -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] 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... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.016s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -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] @@ -4452,165 +4488,165 @@ 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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +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... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.002s] 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] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.004s] 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... [0.002s] +Building reference seed array... [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 6/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query 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 7/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.006s] 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] +Building reference seed array... [0.006s] +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 7/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query 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] -Searching alignments... [0s] +Searching alignments... [0.004s] 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... [0.009s] +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... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +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 8/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] +Building reference 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 8/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query 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 8/16, 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 9/16, 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... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 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... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.005s] -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 9/16, index chunk 4/4. Building reference seed array... [0.005s] -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 10/16, index chunk 1/4. -Building reference 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 10/16, 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... [0.005s] 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 10/16, index chunk 3/4. 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... [0s] +Searching alignments... [0.002s] 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 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 11/16, index chunk 1/4. -Building reference seed array... [0.003s] -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... [0.005s] 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... [0.003s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +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... [0.004s] @@ -4620,155 +4656,155 @@ 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 query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.005s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.003s] +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... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] +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... [0.004s] -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 12/16, 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] +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 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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, 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 13/16, 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... [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 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] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. -Building reference seed array... [0.003s] -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] +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 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.003s] -Building query seed array... [0.001s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.002s] +Computing hash join... [0.003s] +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 3/4. -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... [0s] +Searching alignments... [0.005s] 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 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 15/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] 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 query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.003s] 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 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 15/16, index chunk 4/4. -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... [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 query seed array... [0.001s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.007s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -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] +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... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.006s] +Computing hash join... [0.004s] 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... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.15s] +Computing alignments... [0.193s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -4778,113 +4814,113 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.954s +Total time = 0.98s 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.6OycLsGn47/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.M86lnC5iOP/C.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) Block size = 2000000000 Opening the input file... [0s] Opening the output file... [0s] -Loading query sequences... [0.001s] -Masking queries... [0.004s] +Loading query sequences... [0s] +Masking queries... [0.003s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.015s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.012s] +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 reference seed array... [0.001s] Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [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... [0.002s] -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... [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... [0.005s] +Building reference seed array... [0.001s] +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 1/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.006s] +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 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +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 2/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query 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 2/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +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 2/16, 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 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -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... [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... [0.003s] +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 3/16, index chunk 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -4897,14 +4933,14 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] +Computing hash join... [0.005s] 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... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -4912,266 +4948,266 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4. Building reference seed array... [0.001s] -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 5/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] +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 5/16, index chunk 2/4. Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.006s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] 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... [0.003s] +Building reference 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 6/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.01s] 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] +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 6/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] 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... [0.003s] +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 7/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.004s] Building query seed array... [0.004s] -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 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.004s] +Building reference seed array... [0.002s] +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 7/16, index chunk 3/4. -Building reference seed array... [0.002s] +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... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +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 8/16, index chunk 1/4. Building reference seed array... [0.002s] -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... [0.002s] -Building query seed array... [0.003s] +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 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... [0.001s] 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... [0.002s] -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... [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 reference seed array... [0.001s] +Building query seed array... [0.006s] 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 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... [0.007s] +Building query seed array... [0.004s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building 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 9/16, index chunk 4/4. -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... [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] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.006s] +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 10/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.001s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.001s] 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... [0.009s] +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... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +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... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.006s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +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... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.007s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] +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 11/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query 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] +Masking low complexity seeds... [0.004s] 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 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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.008s] +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 12/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +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 12/16, index chunk 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] 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 reference seed array... [0.001s] +Building query seed array... [0.006s] 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 13/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.009s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0.001s] -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 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.004s] +Building query seed array... [0.008s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -5184,78 +5220,78 @@ 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] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.01s] +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... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0s] +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 15/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.007s] 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 reference seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.005s] +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 15/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.001s] +Building reference seed array... [0.009s] Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.006s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.321s] +Computing alignments... [0.297s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5265,17 +5301,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.033s +Total time = 1.163s 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.6OycLsGn47/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.M86lnC5iOP/M.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -5285,190 +5321,190 @@ Loading query sequences... [0s] Masking queries... [0.004s] Algorithm: Double-indexed -Building query histograms... [0.007s] +Building query histograms... [0.006s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.007s] +Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +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... [0.004s] -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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.007s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.004s] +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 1/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] +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 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +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 2/16, index chunk 2/4. -Building reference seed array... [0.002s] -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 2/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -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 2/16, index chunk 4/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] 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... [0.002s] +Building reference seed array... [0.004s] +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 3/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.001s] +Computing hash join... [0.005s] 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 query seed array... [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 3/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] 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... [0.004s] -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... [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 query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] 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 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +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 4/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] 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 5/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference 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 5/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] +Computing hash join... [0.004s] 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 4/4. -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 6/16, index chunk 1/4. -Building reference seed array... [0.003s] -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... [0.001s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +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... [0.004s] -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] +Searching alignments... [0.005s] 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 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 6/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0.005s] 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 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] +Masking low complexity seeds... [0.003s] 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 reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5476,37 +5512,37 @@ 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 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 7/16, index chunk 4/4. Building reference seed array... [0.004s] Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.004s] 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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] +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 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... [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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.001s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. @@ -5517,168 +5553,168 @@ 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... [0.004s] -Building query seed array... [0.002s] -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... [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... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.004s] 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... [0.001s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.006s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.003s] 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 reference 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 10/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.009s] Building query seed array... [0.001s] -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 10/16, index chunk 2/4. -Building reference 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] +Searching alignments... [0.003s] 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... [0.001s] +Building reference seed array... [0.009s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.002s] 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... [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 11/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.002s] 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... [0.001s] +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 11/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query 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 11/16, index chunk 4/4. -Building reference seed array... [0.003s] -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... [0.001s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +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 12/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +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 12/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.001s] 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... [0.003s] +Building reference seed array... [0.004s] Building query seed array... [0.001s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4. Building reference seed array... [0.004s] -Building query seed array... [0.002s] +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 13/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.009s] 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 13/16, 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... [0.004s] 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 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.009s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] -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] +Searching alignments... [0.002s] 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... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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 reference seed array... [0.008s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -5686,63 +5722,63 @@ 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... [0.002s] +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 15/16, index chunk 2/4. -Building reference seed array... [0.003s] -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... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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 query seed array... [0.002s] +Building reference seed array... [0.007s] +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 15/16, 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... [0.001s] 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... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.002s] 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... [0.001s] -Building query seed array... [0.001s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +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... [0.004s] -Building query seed array... [0.002s] +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 16/16, index chunk 4/4. Building reference seed array... [0.003s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.002s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.172s] +Computing alignments... [0.154s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -5752,119 +5788,119 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.889s +Total time = 1.042s 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.6OycLsGn47/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.M86lnC5iOP/C.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) Block size = 2000000000 Opening the input file... [0s] Opening the output file... [0s] -Loading query sequences... [0.001s] -Masking queries... [0.008s] +Loading query sequences... [0s] +Masking queries... [0.004s] Algorithm: Double-indexed -Building query histograms... [0.011s] +Building query histograms... [0.015s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0.004s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +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... [0.002s] -Building query seed array... [0.004s] +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] -Deallocating memory... [0s] +Deallocating memory... [0.001s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.004s] +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 1/16, index chunk 3/4. Building reference seed array... [0.001s] -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 4/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] 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] +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... [0.001s] -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... [0.001s] -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 2/16, index chunk 4/4. -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... [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... [0.003s] +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 3/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.006s] +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 3/16, index chunk 3/4. -Building reference seed array... [0.002s] -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 3/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0s] +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 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] @@ -5872,147 +5908,147 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0.004s] 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... [0.003s] 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 5/16, index chunk 1/4. Building reference seed array... [0.001s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.002s] +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 5/16, index chunk 2/4. -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... [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] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.01s] +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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, 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] 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... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.013s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] 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... [0s] +Searching alignments... [0.005s] 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 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... [0.003s] 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... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +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 7/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.005s] +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... [0.001s] -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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +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 8/16, 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] +Masking low complexity seeds... [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... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.004s] +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 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] 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... [0.003s] +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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -6025,211 +6061,211 @@ 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 query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.01s] +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 10/16, index chunk 1/4. -Building reference 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... [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 query seed array... [0.003s] -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... [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... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] +Computing hash join... [0.008s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] 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... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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 query seed array... [0.003s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] 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 11/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.004s] +Computing hash join... [0.007s] +Masking low complexity seeds... [0.002s] +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... [0.001s] -Building query seed array... [0.004s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] 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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.006s] 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 12/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.003s] 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 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 12/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] 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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +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 13/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference 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 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] 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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.002s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] 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... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] +Computing hash join... [0.004s] 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... [0.002s] -Building query seed array... [0.004s] +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... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.004s] +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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.006s] +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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] +Computing hash join... [0.004s] 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... [0.005s] +Building reference seed array... [0.006s] +Building query seed array... [0.007s] 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 reference seed array... [0.008s] +Building query seed array... [0.002s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] 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... [0.008s] Building query seed array... [0.005s] 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 16/16, index chunk 1/4. -Building reference seed array... [0.002s] -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... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [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... [0.001s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.002s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.002s] -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] +Searching alignments... [0.002s] 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 reference seed array... [0.001s] Building query seed array... [0.003s] -Computing hash join... [0s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.371s] +Computing alignments... [0.287s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6239,17 +6275,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.143s +Total time = 1.14s 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.6OycLsGn47/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.M86lnC5iOP/C2.faa.vs.C.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C.faa.diamond (type: Diamond database, sequences: 109, letters: 51213) @@ -6259,36 +6295,36 @@ Loading query sequences... [0s] Masking queries... [0s] Algorithm: Double-indexed -Building query histograms... [0s] +Building query histograms... [0.001s] Seeking in database... [0s] -Loading reference sequences... [0s] -Masking reference... [0.007s] +Loading reference sequences... [0.001s] +Masking reference... [0.002s] Initializing temporary storage... [0s] -Building reference histograms... [0.025s] +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 reference seed array... [0.006s] 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... [0.005s] +Building reference seed array... [0.001s] Building query seed array... [0s] -Computing hash join... [0s] +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 3/4. -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] +Searching alignments... [0.004s] 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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6302,255 +6338,255 @@ 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... [0.005s] +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 2/16, 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] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.004s] 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... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.005s] 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... [0.003s] +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 3/16, 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 3/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +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 4/16, index chunk 2/4. -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 4/16, index chunk 3/4. -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 4/16, index chunk 4/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.011s] 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... [0.005s] +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 5/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +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 5/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.003s] 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 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 6/16, index chunk 1/4. Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] +Building query seed array... [0.003s] +Computing hash join... [0.007s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.005s] 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 reference seed array... [0.001s] Building query seed array... [0s] 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 6/16, index chunk 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.01s] 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 7/16, 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] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.006s] 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... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.007s] 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 query seed array... [0s] +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... [0.002s] 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] +Building reference seed array... [0.006s] +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 8/16, index chunk 2/4. -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 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +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 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 query 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] +Searching alignments... [0.012s] 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 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 9/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.002s] +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... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] +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 10/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +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... [0.001s] 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... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.003s] 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 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 10/16, index chunk 4/4. -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] +Masking low complexity seeds... [0.004s] 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... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.003s] +Computing hash join... [0.002s] +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 2/4. @@ -6558,31 +6594,31 @@ 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 11/16, 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] +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 11/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] 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... [0.002s] Building query seed array... [0s] -Computing hash join... [0s] +Computing hash join... [0.003s] 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... [0.004s] +Building reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -6596,127 +6632,127 @@ 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 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 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 13/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] 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... [0.002s] 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... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.006s] +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 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.004s] 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... [0s] +Building reference seed array... [0.011s] +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 14/16, index chunk 3/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.007s] Building query seed array... [0s] -Computing hash join... [0s] +Computing hash join... [0.003s] 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... [0.005s] +Building reference seed array... [0.006s] Building query seed array... [0s] 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 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 15/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +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 15/16, 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] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] 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 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 16/16, index chunk 1/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.006s] 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 16/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.008s] 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... [0.005s] +Building reference seed array... [0.007s] Building query seed array... [0s] 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 16/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.008s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.008s] +Computing alignments... [0.052s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -6726,27 +6762,27 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.636s +Total time = 0.789s 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.6OycLsGn47/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.M86lnC5iOP/C.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) Block size = 2000000000 Opening the input file... [0s] Opening the output file... [0s] -Loading query sequences... [0.001s] -Masking queries... [0.005s] +Loading query sequences... [0s] +Masking queries... [0.006s] Algorithm: Double-indexed -Building query histograms... [0.01s] +Building query histograms... [0.009s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -6755,294 +6791,294 @@ 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... [0.005s] +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 1/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.007s] +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 3/4. Building reference seed array... [0s] -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 1/16, 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... [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... [0.003s] +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 2/16, 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 2/16, 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 2/16, 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... [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... [0.004s] +Building reference seed array... [0.009s] +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... [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... [0.003s] 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... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.005s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.007s] 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... [0.001s] 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 4/16, 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] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.004s] 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 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 3/4. 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] 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... [0.002s] 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 5/16, index chunk 1/4. -Building reference seed array... [0s] +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... [0.002s] 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 query seed array... [0.004s] +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 5/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.007s] +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 5/16, index chunk 4/4. 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... [0.002s] 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] +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 6/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] 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... [0.002s] +Building query seed array... [0.003s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.005s] 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... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.006s] 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 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 3/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +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... [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] +Searching alignments... [0.006s] 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] -Computing hash join... [0s] +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 8/16, index chunk 2/4. -Building reference seed array... [0s] +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... [0.002s] 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... [0.003s] +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 8/16, 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... [0.006s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.002s] 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... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.001s] +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 9/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.004s] +Building query seed array... [0.003s] 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 3/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.003s] 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... [0.003s] +Building reference seed array... [0.001s] +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 10/16, index chunk 1/4. -Building reference seed array... [0s] -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] +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 2/4. 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] +Masking low complexity seeds... [0.005s] 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 reference seed array... [0.002s] +Building query seed array... [0.003s] 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 10/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.003s] -Computing hash join... [0s] +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 11/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] +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 11/16, index chunk 2/4. -Building reference seed array... [0s] -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] @@ -7050,75 +7086,75 @@ 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] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] 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... [0.004s] +Building reference seed array... [0.003s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] 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... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] 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... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +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... [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 12/16, 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] +Masking low complexity seeds... [0.001s] +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... [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 13/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] +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 13/16, 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... [0s] +Searching alignments... [0.004s] 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... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -7126,57 +7162,57 @@ 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... [0.004s] -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 14/16, 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... [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... [0.005s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] 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... [0.002s] +Building query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] 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... [0.006s] +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... [0s] -Building query seed array... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.002s] +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... [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 16/16, index chunk 1/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -7185,25 +7221,25 @@ Building query seed array... [0.004s] 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 16/16, 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] +Masking low complexity seeds... [0.002s] 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... [0.004s] -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] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.008s] +Computing alignments... [0.021s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7213,17 +7249,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.652s +Total time = 0.745s 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.6OycLsGn47/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.M86lnC5iOP/L.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -7231,466 +7267,466 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.003s] +Masking queries... [0.001s] Algorithm: Double-indexed Building query histograms... [0.01s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.009s] Initializing temporary storage... [0s] -Building reference histograms... [0.027s] +Building reference histograms... [0.021s] Allocating buffers... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4. Building reference seed array... [0.004s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.003s] 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... [0.002s] +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 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... [0.005s] +Computing hash join... [0.001s] 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 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... [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... [0.005s] +Building reference seed array... [0.004s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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] +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... [0.001s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. -Building reference seed array... [0.005s] -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 3/16, index chunk 1/4. -Building reference seed array... [0.005s] +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 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... [0.001s] +Searching alignments... [0.002s] 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] +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... [0.004s] -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] +Searching alignments... [0.002s] 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... [0.002s] +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 4/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.004s] +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... [0.006s] Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.006s] 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] +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 5/16, index chunk 1/4. Building reference seed array... [0.003s] -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 5/16, index chunk 2/4. 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... [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... [0.002s] -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... [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... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] 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 6/16, 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... [0.001s] +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... [0.004s] -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 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... [0.006s] 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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] 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] +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... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.002s] 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 query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] 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 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] +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 8/16, index chunk 1/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.011s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, 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 8/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +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 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... [0.007s] 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 9/16, index chunk 1/4. -Building reference seed array... [0.003s] -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... [0.005s] 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... [0.008s] +Building query seed array... [0.001s] 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 9/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [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] -Deallocating memory... [0s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.002s] +Deallocating memory... [0.003s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -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] -Searching alignments... [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... [0.004s] +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] -Deallocating memory... [0s] +Deallocating memory... [0.003s] 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] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] -Deallocating memory... [0s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0s] +Deallocating memory... [0.001s] 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... [0.005s] Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +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... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.008s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4. -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] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.001s] +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... [0.004s] Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +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... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.006s] 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 11/16, 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 12/16, index chunk 1/4. -Building reference seed array... [0.003s] -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] +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 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 12/16, index chunk 3/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.003s] +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 13/16, index chunk 1/4. -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... [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... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.004s] 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... [0.002s] Building query seed array... [0.002s] -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 13/16, index chunk 4/4. -Building reference seed array... [0.004s] +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 14/16, 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 14/16, 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 14/16, 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] +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 14/16, index chunk 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.001s] +Building reference seed array... [0.012s] +Building query seed array... [0.004s] 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 15/16, index chunk 1/4. -Building reference seed array... [0.004s] -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... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.008s] +Building query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.008s] 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... [0.002s] +Building reference seed array... [0.005s] +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 15/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.008s] +Building query seed array... [0.007s] 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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] 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... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.004s] 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 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 4/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.009s] +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... [0.619s] +Computing alignments... [0.474s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -7700,17 +7736,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.336s +Total time = 1.374s 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.6OycLsGn47/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.M86lnC5iOP/E.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -7718,182 +7754,182 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.008s] +Masking queries... [0.003s] Algorithm: Double-indexed -Building query histograms... [0.027s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.002s] 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... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.004s] 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... [0.005s] +Building reference seed array... [0.011s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building query seed array... [0.006s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] +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 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference 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 2/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +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... [0.011s] 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 reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.004s] 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 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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +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 3/16, 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... [0.002s] 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 3/4. Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.006s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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 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... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. -Building reference seed array... [0.002s] +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... [0.001s] +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] +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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.004s] +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 4/16, 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... [0.01s] 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... [0.002s] -Building query seed array... [0.003s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] +Computing hash join... [0.003s] 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... [0.002s] +Building reference seed array... [0.001s] 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 5/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.007s] 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] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] +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 6/16, index chunk 1/4. -Building reference 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... [0.001s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. -Building reference seed array... [0.002s] -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... [0.001s] 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... [0.005s] +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 6/16, index chunk 4/4. -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... [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... [0.002s] @@ -7903,281 +7939,281 @@ Searching alignments... [0.001s] 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... [0.005s] +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] 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 reference seed array... [0.011s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.003s] +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] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.006s] +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 8/16, 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... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.006s] +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 reference seed array... [0.006s] +Building query seed array... [0.002s] Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.007s] 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... [0.005s] +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 8/16, 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... [0.002s] +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 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.011s] +Computing hash join... [0.003s] 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... [0.003s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.007s] +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 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.004s] 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... [0.005s] +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 10/16, index chunk 3/4. -Building reference seed array... [0.002s] -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... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.006s] Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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... [0.001s] -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] 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... [0.002s] 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... [0.002s] -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... [0.006s] 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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] 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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] 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... [0.002s] -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... [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... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.003s] +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... [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... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] 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 13/16, index chunk 3/4. Building reference seed array... [0.001s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.002s] 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 reference seed array... [0.007s] 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 14/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.007s] 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] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.005s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.007s] +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] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.002s] +Computing hash join... [0.003s] 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 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0s] +Masking low complexity seeds... [0.001s] 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... [0.005s] +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... [0.002s] -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... [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... [0.002s] -Building query seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.007s] 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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] 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 16/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.008s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.004s] 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 reference seed array... [0.001s] Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.004s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [1.092s] +Computing alignments... [0.814s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8187,476 +8223,476 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.988s +Total time = 1.706s 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.6OycLsGn47/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.M86lnC5iOP/M.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) Block size = 2000000000 Opening the input file... [0s] -Opening the output file... [0s] +Opening the output file... [0.002s] Loading query sequences... [0s] Masking queries... [0.002s] Algorithm: Double-indexed -Building query histograms... [0.012s] +Building query histograms... [0.014s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.003s] +Masking reference... [0.006s] Initializing temporary storage... [0s] -Building reference histograms... [0.027s] +Building reference histograms... [0.016s] 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... [0.002s] +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... [0.004s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [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 query seed array... [0.002s] +Building reference seed array... [0.002s] +Building query seed array... [0.008s] 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... [0.003s] -Building query seed array... [0.002s] +Building reference 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 2/16, index chunk 1/4. -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 2/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] 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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.005s] 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] +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... [0.005s] -Building query seed array... [0.002s] +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 3/16, 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... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.002s] +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... [0.002s] -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 3/16, index chunk 4/4. -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... [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... [0.01s] +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 4/16, 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 4/16, 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... [0.013s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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 4/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.006s] Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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 5/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.015s] +Building query seed array... [0.008s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.007s] +Building query seed array... [0.006s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +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] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] +Computing hash join... [0.003s] 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 5/16, 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... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.006s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.007s] +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... [0.003s] +Building query seed array... [0.004s] +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 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... [0.003s] +Building query seed array... [0.004s] +Computing hash join... [0.007s] 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... [0.004s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] +Building reference seed array... [0.007s] +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... [0.004s] -Building query seed array... [0.002s] +Building reference 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] +Deallocating memory... [0.002s] 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] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.001s] 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... [0.003s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.003s] 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... [0.003s] +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 8/16, 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... [0.001s] +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 reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.007s] 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] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.003s] 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... [0.001s] +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 9/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] 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 9/16, index chunk 2/4. -Building reference seed array... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.008s] 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] +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... [0.004s] 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... [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... [0.002s] 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] -Computing hash join... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.004s] +Computing hash join... [0.006s] 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... [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 10/16, 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] 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 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] +Searching alignments... [0.005s] 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... [0.007s] 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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.005s] 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... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.002s] 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... [0.005s] -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] +Masking low complexity seeds... [0.002s] +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... [0.003s] -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 12/16, 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] +Building reference seed array... [0.006s] +Building query seed array... [0.003s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.001s] 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... [0.005s] -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 12/16, index chunk 4/4. -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... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] 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... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.004s] +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... [0.003s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.011s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.006s] 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... [0.005s] -Building query seed array... [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] 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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.007s] +Computing hash join... [0.004s] 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 14/16, index chunk 1/4. -Building reference seed array... [0.005s] -Building query seed array... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.009s] +Computing hash join... [0.001s] 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 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] +Building reference seed array... [0.006s] +Building query seed array... [0.008s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.002s] 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... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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... [0.005s] -Building query seed array... [0.002s] +Building reference seed array... [0.006s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.001s] 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... [0.004s] -Building query seed array... [0.002s] +Building reference seed array... [0.007s] +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 15/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.006s] 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 15/16, 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... [0s] +Searching alignments... [0.008s] 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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.005s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.003s] 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... [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... [0.001s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4. -Building reference seed array... [0.005s] +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 16/16, 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... [0.005s] 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 16/16, 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] @@ -8664,7 +8700,7 @@ Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.62s] +Computing alignments... [0.469s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -8674,484 +8710,484 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.507s +Total time = 1.478s 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.6OycLsGn47/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.M86lnC5iOP/E.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) Block size = 2000000000 Opening the input file... [0s] Opening the output file... [0s] -Loading query sequences... [0.001s] -Masking queries... [0.004s] +Loading query sequences... [0s] +Masking queries... [0.005s] Algorithm: Double-indexed -Building query histograms... [0.026s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.005s] Initializing temporary storage... [0s] -Building reference histograms... [0.014s] +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... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.006s] +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... [0.002s] -Building query 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... [0.002s] +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... [0.002s] -Building query seed array... [0.004s] +Building reference seed array... [0.003s] +Building query seed array... [0.007s] 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 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... [0.002s] +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 reference seed array... [0.001s] +Building query seed array... [0.001s] 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 2/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.007s] +Computing hash join... [0.002s] 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... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] 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 2/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.008s] Building query seed array... [0.004s] 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 3/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.006s] +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... [0.001s] -Building query 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 3/16, index chunk 3/4. -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] +Masking low complexity seeds... [0.005s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0.006s] 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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] 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 4/16, index chunk 2/4. -Building reference 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... [0.001s] +Masking low complexity seeds... [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... [0.002s] -Building query seed array... [0.005s] -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] 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 reference seed array... [0.001s] +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 5/16, 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... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [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] -Building query seed array... [0.005s] +Building reference seed array... [0s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0.005s] 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... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.008s] Building query seed array... [0.004s] 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 6/16, 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... [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 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.003s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.003s] 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... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.007s] +Building query seed array... [0.008s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] +Computing hash join... [0.006s] 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 3/4. -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... [0.01s] +Computing hash join... [0.004s] 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 7/16, index chunk 4/4. Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.01s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4. -Building reference seed array... [0.002s] -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... [0.001s] +Searching alignments... [0.002s] 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... [0.005s] Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.003s] 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] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] +Computing hash join... [0.002s] 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... [0.002s] -Building query seed array... [0.004s] +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 9/16, 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... [0.004s] +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 9/16, 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... [0.003s] 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 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... [0.01s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.002s] +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 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.006s] +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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.006s] +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 10/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.007s] 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 10/16, index chunk 4/4. Building reference seed array... [0.001s] -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] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.004s] 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... [0.003s] +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 11/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0.001s] +Building reference seed array... [0.007s] +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 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.006s] 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... [0.005s] +Building reference seed array... [0.007s] +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 12/16, 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... [0.008s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.006s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] -Deallocating memory... [0s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.001s] +Deallocating memory... [0.004s] 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... [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... [0s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.008s] +Computing hash join... [0.007s] 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... [0.002s] -Building query seed array... [0.005s] +Building reference seed array... [0.004s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.007s] 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 reference seed array... [0.001s] +Building query seed array... [0.006s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.003s] +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... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.007s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] 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... [0.003s] +Building query seed array... [0.015s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.005s] 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 reference seed array... [0.008s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.009s] 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... [0.003s] 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 14/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.005s] +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] +Masking low complexity seeds... [0.002s] +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... [0.004s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] +Building query seed array... [0.005s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.002s] 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... [0.005s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] 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... [0.001s] +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... [0.002s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.006s] +Computing hash join... [0.009s] 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 15/16, index chunk 4/4. 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] +Building query seed array... [0.009s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.006s] Building query seed array... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.006s] 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 reference seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.004s] 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 reference seed array... [0.011s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.004s] 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... [0.004s] +Building reference seed array... [0.005s] +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... [1.162s] +Computing alignments... [1.063s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9161,17 +9197,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 2.091s +Total time = 2.115s 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.6OycLsGn47/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.M86lnC5iOP/C2.faa.vs.E.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/E.faa.diamond (type: Diamond database, sequences: 72, letters: 54509) @@ -9184,83 +9220,83 @@ Building query histograms... [0s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.007s] +Masking reference... [0.003s] Initializing temporary storage... [0s] -Building reference histograms... [0.011s] +Building reference histograms... [0.016s] 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 reference seed array... [0.008s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.01s] 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 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... [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... [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... [0.005s] +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 1/4. -Building reference seed array... [0.005s] -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 2/16, index chunk 2/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.009s] Building query seed array... [0s] -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 2/16, index chunk 3/4. -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 2/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +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... [0.005s] -Building query seed array... [0s] +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 3/16, 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 3/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -9274,15 +9310,15 @@ 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.006s] +Computing hash join... [0.008s] +Masking low complexity seeds... [0.003s] 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... [0s] -Computing hash join... [0s] +Building reference seed array... [0.015s] +Building query seed array... [0.006s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -9291,115 +9327,115 @@ 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 4/16, index chunk 4/4. -Building reference seed array... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.002s] +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... [0.002s] -Building query seed array... [0s] +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 2/4. -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... [0.003s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.004s] +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... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.003s] 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... [0s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.003s] 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... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.001s] 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 6/16, index chunk 2/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] +Building reference seed array... [0.01s] +Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +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... [0.005s] -Building query seed array... [0s] +Building reference seed array... [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 6/16, 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] 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 reference seed array... [0.002s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] 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 7/16, index chunk 3/4. -Building reference seed array... [0.005s] +Building reference seed array... [0.001s] Building query seed array... [0s] -Computing hash join... [0s] +Computing hash join... [0.002s] 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 4/4. -Building reference seed array... [0.003s] -Building query 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] +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... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.008s] +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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -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] @@ -9407,62 +9443,62 @@ 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.002s] 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... [0.009s] Building query seed array... [0s] 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 9/16, index chunk 2/4. -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] +Searching alignments... [0.002s] 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] +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 9/16, index chunk 4/4. -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 10/16, index chunk 1/4. -Building reference seed array... [0.003s] +Building reference seed array... [0.002s] Building query seed array... [0s] -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 10/16, index chunk 2/4. -Building reference seed array... [0.003s] -Building query seed array... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.009s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.002s] 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 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 10/16, index chunk 4/4. -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] @@ -9471,54 +9507,54 @@ 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] +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 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 11/16, index chunk 3/4. -Building reference seed array... [0.004s] +Building reference seed array... [0.007s] 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... [0.005s] -Building query seed array... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +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... [0.003s] -Building query seed array... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.002s] 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 12/16, 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] 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 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 12/16, index chunk 4/4. -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] @@ -9526,97 +9562,97 @@ 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] +Building query seed array... [0.006s] +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 13/16, 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 13/16, index chunk 3/4. -Building reference seed array... [0.005s] -Building query 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] +Masking low complexity seeds... [0.002s] +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... [0.003s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.005s] +Computing hash join... [0.002s] 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 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] +Searching alignments... [0.003s] 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... [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 14/16, index chunk 3/4. -Building reference seed array... [0.004s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.009s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] 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 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... [0.005s] +Building reference seed array... [0.012s] 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... [0.003s] -Building query seed array... [0s] -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... [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... [0s] +Building reference seed array... [0.008s] +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... [0s] -Computing hash join... [0s] +Building query seed array... [0.007s] +Computing hash join... [0.007s] 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... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] 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 16/16, 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] @@ -9624,21 +9660,21 @@ 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... [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 16/16, index chunk 4/4. -Building reference seed array... [0.003s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.009s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.009s] +Computing alignments... [0.03s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -9648,17 +9684,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.616s +Total time = 0.816s 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.6OycLsGn47/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.M86lnC5iOP/E.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -9666,9 +9702,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.006s] +Masking queries... [0.004s] Algorithm: Double-indexed -Building query histograms... [0.027s] +Building query histograms... [0.013s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -9677,48 +9713,48 @@ 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... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.004s] 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] +Building reference seed array... [0.003s] +Building query seed array... [0.006s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +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... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.005s] +Building query seed array... [0.003s] 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 1/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.002s] +Computing hash join... [0.005s] 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... [0.005s] +Building reference seed array... [0.004s] +Building query seed array... [0.008s] 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... [0s] 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 2/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.003s] Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -9726,168 +9762,168 @@ 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... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.006s] 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... [0.005s] +Building reference seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4. Building reference seed array... [0s] Building query seed array... [0.004s] 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 3/16, index chunk 3/4. 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 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] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.009s] 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... [0.005s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.002s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.004s] 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... [0.005s] +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 4/16, index chunk 3/4. 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] +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... [0s] -Building query seed array... [0.005s] +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 1/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +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 2/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +Building query seed array... [0.006s] 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 3/4. Building reference seed array... [0s] -Building query seed array... [0.004s] -Computing hash join... [0s] +Building query seed array... [0.008s] +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 5/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +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 6/16, index chunk 1/4. -Building reference seed array... [0s] -Building query 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 6/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +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 6/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.008s] 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... [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] +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... [0s] -Building query 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] +Deallocating memory... [0.001s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +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 7/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building query seed array... [0.01s] +Computing hash join... [0.008s] 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 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... [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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.006s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.003s] 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 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 3/4. 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] @@ -9903,71 +9939,71 @@ Building reference seed array... [0s] Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.003s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.01s] 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 9/16, index chunk 3/4. Building reference seed array... [0s] Building query seed array... [0.005s] -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 9/16, index chunk 4/4. -Building reference seed array... [0s] -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] +Searching alignments... [0.004s] 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... [0.005s] +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 10/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +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 10/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +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 10/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +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 11/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.002s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +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... [0s] @@ -9978,63 +10014,63 @@ 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... [0.005s] +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... [0s] -Building query seed array... [0.005s] +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 12/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.003s] +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 12/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.005s] -Computing hash join... [0s] +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 12/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +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 13/16, 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] +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... [0s] -Building query seed array... [0.005s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [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] -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... [0s] -Deallocating memory... [0s] +Deallocating memory... [0.002s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -10044,88 +10080,88 @@ Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] -Deallocating memory... [0s] +Searching alignments... [0.001s] +Deallocating memory... [0.003s] 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... [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 14/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.007s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.006s] 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... [0.005s] +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 15/16, index chunk 2/4. Building reference seed array... [0s] -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 15/16, index chunk 3/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.003s] +Building query seed array... [0.006s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.003s] 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... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4. -Building reference seed array... [0s] -Building query seed array... [0.005s] +Building reference seed array... [0.007s] +Building query seed array... [0.008s] 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 16/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.004s] +Building reference seed array... [0.001s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +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 3/4. -Building reference seed array... [0s] -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] +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... [0s] Building query seed array... [0.005s] -Computing hash join... [0s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.008s] +Computing alignments... [0.019s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10135,17 +10171,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.698s +Total time = 0.843s 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.6OycLsGn47/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.M86lnC5iOP/M.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -10153,388 +10189,388 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.003s] +Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.006s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +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... [0.002s] -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... [0.009s] +Searching alignments... [0.004s] 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 reference seed array... [0.005s] +Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.01s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.004s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] 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 1/16, 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... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.003s] 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] +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... [0.003s] 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... [0.001s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.01s] 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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.002s] +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... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.003s] 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... [0.003s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.008s] 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] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] 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] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] -Deallocating memory... [0s] +Searching alignments... [0.004s] +Deallocating memory... [0.002s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] 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 4/16, 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... [0.004s] +Computing hash join... [0.002s] 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... [0.002s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +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] +Building reference seed array... [0.008s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] -Deallocating memory... [0s] +Searching alignments... [0.007s] +Deallocating memory... [0.005s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.004s] 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... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.006s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.004s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.006s] 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] +Building reference seed array... [0.003s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.003s] 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... [0.01s] 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 6/16, index chunk 2/4. -Building reference seed array... [0.002s] -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... [0.007s] +Searching alignments... [0.008s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.001s] +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] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.002s] +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] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] 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 7/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.014s] 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... [0.007s] +Searching alignments... [0.011s] 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... [0.002s] -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... [0.007s] +Searching alignments... [0.003s] 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 reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.007s] 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... [0.002s] +Building reference seed array... [0.011s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.003s] 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Searching alignments... [0.004s] 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] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] 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 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.004s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.01s] 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... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.004s] 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] +Computing hash join... [0.003s] 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 10/16, 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... [0.007s] +Searching alignments... [0.003s] 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] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.004s] 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 query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.008s] +Searching alignments... [0.005s] 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] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.005s] 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... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.004s] 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... [0.008s] 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... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.008s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.007s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.007s] 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... [0.002s] +Building reference seed array... [0.004s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.007s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.006s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.011s] 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] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.005s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] -Deallocating memory... [0s] +Searching alignments... [0.007s] +Deallocating memory... [0.002s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.006s] 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] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.004s] 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] +Building query seed array... [0.003s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.004s] 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... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -10542,77 +10578,77 @@ 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] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.012s] 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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.01s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.006s] 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... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.007s] +Searching alignments... [0.012s] 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 reference seed array... [0.004s] +Building query seed array... [0.005s] 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 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] 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 16/16, 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] +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] 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] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.004s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.005s] 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 16/16, 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... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.003s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.473s] +Computing alignments... [0.446s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -10622,17 +10658,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.651s +Total time = 1.64s 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.6OycLsGn47/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.M86lnC5iOP/L.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) @@ -10640,438 +10676,438 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.004s] +Masking queries... [0.01s] Algorithm: Double-indexed -Building query histograms... [0.006s] +Building query histograms... [0.017s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +Building reference histograms... [0.022s] 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... [0.006s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.014s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.009s] +Building query seed array... [0.001s] 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 reference seed array... [0.005s] +Building query seed array... [0.011s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Searching alignments... [0.006s] 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... [0.009s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.004s] 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 2/16, index chunk 1/4. Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.003s] 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 2/16, 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... [0.008s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.021s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.007s] +Building query seed array... [0.004s] +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 2/16, 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... [0.008s] +Building reference seed array... [0.008s] +Building query seed array... [0.011s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.003s] 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.009s] 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 3/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.006s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.011s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.01s] 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] +Building reference seed array... [0.008s] +Building query seed array... [0.007s] 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 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... [0.008s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] 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] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.009s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.006s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.012s] +Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.006s] 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... [0.005s] +Building reference seed array... [0.001s] +Building query seed array... [0.007s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.007s] +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... [0.009s] +Building reference seed array... [0.011s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.006s] 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... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.012s] +Building query seed array... [0.009s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.01s] 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... [0.001s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.006s] +Masking low complexity seeds... [0.001s] +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 query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Building reference seed array... [0.006s] +Building query seed array... [0.004s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.01s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.011s] +Building query seed array... [0.004s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.007s] 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... [0.002s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.003s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.007s] +Searching alignments... [0.005s] 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... [0.008s] 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... [0.015s] 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... [0.002s] +Building reference seed array... [0.008s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.008s] +Building query seed array... [0.003s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.004s] 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... [0.008s] +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... [0.007s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Building reference seed array... [0.011s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.011s] 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 reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.014s] 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] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.004s] 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... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.007s] +Computing hash join... [0.006s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +Searching alignments... [0.003s] 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 reference seed array... [0.001s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.003s] 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 9/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0.009s] -Deallocating memory... [0s] +Searching alignments... [0.003s] +Deallocating memory... [0.001s] 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] +Building reference seed array... [0.004s] +Building query seed array... [0.007s] 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 9/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.018s] 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] +Building reference seed array... [0.001s] +Building query seed array... [0.005s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +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... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] +Computing hash join... [0.004s] 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 10/16, index chunk 2/4. 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... [0.006s] +Searching alignments... [0.009s] 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] -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... [0.008s] +Searching alignments... [0.005s] 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] +Building reference seed array... [0.007s] +Building query seed array... [0.01s] 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 11/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] 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 11/16, index chunk 2/4. -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... [0.008s] 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 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... [0.005s] +Searching alignments... [0.01s] 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... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.009s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. Building reference seed array... [0.001s] -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... [0.005s] +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... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.005s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0.005s] -Deallocating memory... [0s] +Searching alignments... [0.004s] +Deallocating memory... [0.003s] 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... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.004s] 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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.008s] +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 13/16, index chunk 1/4. -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... [0.005s] +Searching alignments... [0.012s] 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] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.003s] +Computing hash join... [0.001s] 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 13/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.008s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Searching alignments... [0.004s] 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... [0.008s] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.003s] 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... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] 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 14/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0.001s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] +Computing hash join... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.004s] 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 query seed array... [0.005s] 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 14/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] +Building reference seed array... [0.012s] +Building query seed array... [0.006s] 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 15/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.004s] +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... [0.002s] -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... [0.008s] +Searching alignments... [0.013s] 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... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.008s] +Masking low complexity seeds... [0.003s] +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... [0.002s] +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... [0.004s] +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] +Building reference seed array... [0.003s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0.009s] @@ -11080,26 +11116,26 @@ Building reference seed array... [0.002s] Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.002s] Searching alignments... [0.008s] 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 reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.003s] +Searching alignments... [0.005s] 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... [0.001s] +Building reference seed array... [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] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.47s] +Computing alignments... [0.401s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -11109,17 +11145,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 1.608s +Total time = 1.885s 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.6OycLsGn47/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.M86lnC5iOP/C2.faa.vs.L.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/L.faa.diamond (type: Diamond database, sequences: 40, letters: 26652) @@ -11129,44 +11165,44 @@ Loading query sequences... [0s] Masking queries... [0s] Algorithm: Double-indexed -Building query histograms... [0s] +Building query histograms... [0.004s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0.004s] +Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +Building reference histograms... [0.015s] 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... [0s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 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... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.003s] 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... [0s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.004s] +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 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.011s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -11179,100 +11215,100 @@ Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] 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 2/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] Building query seed array... [0s] -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 3/16, 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... [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 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 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 3/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.004s] +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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.005s] 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 2/4. Building reference seed array... [0.002s] -Building query seed array... [0s] +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 4/16, 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 4/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] 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 5/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.012s] +Building query seed array... [0.003s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [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... [0.002s] +Building reference seed array... [0.01s] Building query seed array... [0s] -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 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] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] @@ -11281,28 +11317,28 @@ 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 6/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +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... [0.001s] -Building query seed array... [0s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.004s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.005s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4. Building reference seed array... [0.001s] @@ -11313,280 +11349,280 @@ 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.008s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.006s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.012s] Building query seed array... [0s] -Computing hash join... [0s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.007s] 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... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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... [0s] 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 8/16, 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] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] -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 8/16, 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] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4. -Building reference seed array... [0.001s] +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... [0.004s] 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... [0s] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +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 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... [0.002s] +Building reference seed array... [0.01s] Building query seed array... [0s] 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 10/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +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 10/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.002s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.006s] 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... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.007s] 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... [0s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.009s] +Computing hash join... [0.002s] 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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +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 11/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +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 11/16, 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] +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... [0.008s] Building query seed array... [0s] 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 12/16, 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] +Searching alignments... [0.003s] 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... [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 12/16, index chunk 3/4. -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 12/16, index chunk 4/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.017s] 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 13/16, index chunk 1/4. -Building reference seed array... [0.002s] -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... [0.008s] +Computing hash join... [0.003s] +Masking low complexity seeds... [0.003s] +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... [0.002s] +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... [0.007s] 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 reference seed array... [0.007s] Building query seed array... [0s] -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 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] 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... [0s] +Building reference seed array... [0.009s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.006s] +Building query seed array... [0.002s] +Computing hash join... [0.003s] +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... [0.001s] -Building query 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] +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... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.007s] +Building query seed array... [0.007s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] 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 reference seed array... [0.008s] Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.002s] +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... [0.001s] -Building query seed array... [0s] +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 15/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.006s] +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 15/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference 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 16/16, 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... [0s] +Searching alignments... [0.008s] 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 reference seed array... [0.012s] Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.011s] 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 reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +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... [0s] +Building query seed array... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.007s] +Computing alignments... [0.018s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -11596,17 +11632,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.48s +Total time = 0.918s 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.6OycLsGn47/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.M86lnC5iOP/L.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -11614,105 +11650,105 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.009s] Algorithm: Double-indexed -Building query histograms... [0.007s] +Building query histograms... [0.01s] Seeking in database... [0s] Loading reference sequences... [0s] -Masking reference... [0s] +Masking reference... [0.001s] Initializing temporary storage... [0s] -Building reference histograms... [0s] +Building reference histograms... [0.001s] 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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Building reference seed array... [0.001s] +Building query seed array... [0.007s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Searching alignments... [0.009s] 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] -Computing hash join... [0s] +Building query seed array... [0.003s] +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 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... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.012s] 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 2/16, 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] +Searching alignments... [0.004s] 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... [0.002s] +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 2/16, index chunk 4/4. -Building reference seed array... [0s] -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] +Searching alignments... [0.005s] 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] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.01s] +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 2/4. 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 3/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.008s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.003s] 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 reference seed array... [0.001s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4. Building reference seed array... [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... [0.003s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4. Building reference seed array... [0s] @@ -11723,146 +11759,146 @@ 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... [0.001s] +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 4/16, 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... [0.002s] 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... [0.002s] +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 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.003s] +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 5/16, index chunk 3/4. -Building reference seed array... [0s] -Building query 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] 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 query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.001s] +Computing hash join... [0.002s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.006s] 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] -Computing hash join... [0s] +Building reference seed array... [0.004s] +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 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] -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 6/16, index chunk 3/4. 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] +Searching alignments... [0.005s] 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... [0.002s] +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 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 7/16, 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] +Searching alignments... [0.003s] 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 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] +Masking low complexity seeds... [0.002s] +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... [0s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.006s] 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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.003s] +Building query seed array... [0.003s] +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 8/16, index chunk 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.008s] 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 8/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 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] +Searching alignments... [0.005s] 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... [0.001s] +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 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.003s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -11870,76 +11906,76 @@ 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... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +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... [0.002s] 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 10/16, index chunk 2/4. Building reference seed array... [0s] Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.003s] 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 reference seed array... [0.005s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] 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... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.001s] +Searching alignments... [0.005s] 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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +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 11/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0.007s] +Computing hash join... [0.003s] +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... [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 reference 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 1/4. -Building reference seed array... [0s] -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 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.001s] Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -11947,28 +11983,28 @@ 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] +Masking low complexity seeds... [0.002s] 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 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 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... [0.004s] +Building query seed array... [0.002s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -11978,67 +12014,67 @@ 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 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] +Masking low complexity seeds... [0.006s] +Searching alignments... [0.003s] 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... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] 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] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.006s] 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] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] 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... [0.002s] -Computing hash join... [0s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] +Computing hash join... [0.004s] 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 reference seed array... [0.003s] +Building query seed array... [0.001s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.007s] 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] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.002s] 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... [0.002s] +Building reference seed array... [0.005s] +Building query seed array... [0.008s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12046,34 +12082,34 @@ 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] -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 16/16, index chunk 2/4. -Building reference seed array... [0s] -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] +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... [0.002s] +Building query seed array... [0.004s] 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 16/16, index chunk 4/4. -Building reference seed array... [0s] -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... [0.003s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.01s] +Computing alignments... [0.023s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -12083,35 +12119,35 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.518s +Total time = 0.764s 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.6OycLsGn47/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.M86lnC5iOP/C2.faa.vs.M.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/M.faa.diamond (type: Diamond database, sequences: 40, letters: 26963) Block size = 2000000000 -Opening the input file... [0s] +Opening the input file... [0.001s] Opening the output file... [0s] Loading query sequences... [0s] Masking queries... [0s] Algorithm: Double-indexed -Building query histograms... [0s] +Building query histograms... [0.006s] Seeking in database... [0s] -Loading reference sequences... [0s] +Loading reference sequences... [0.001s] Masking reference... [0.004s] Initializing temporary storage... [0s] -Building reference histograms... [0.013s] +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... [0.008s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12119,153 +12155,153 @@ Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4. Building reference seed array... [0.001s] -Building query seed array... [0s] +Building query seed array... [0.002s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.004s] 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 2/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.002s] +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... [0.002s] -Building query seed array... [0s] +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 2/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +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 2/16, index chunk 4/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +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 3/16, 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... [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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building reference seed array... [0.001s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] +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 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 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 4/16, index chunk 1/4. -Building reference seed array... [0.002s] +Building reference seed array... [0s] 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 query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +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 4/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.007s] Building query seed array... [0s] -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 4/16, index chunk 4/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +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 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.006s] +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 5/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.011s] +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 4/4. Building reference seed array... [0.002s] -Building query seed array... [0s] +Building query seed array... [0.01s] 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 6/16, index chunk 1/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.006s] +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 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +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 6/16, 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] @@ -12274,68 +12310,68 @@ 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... [0s] -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 7/16, index chunk 1/4. -Building reference seed array... [0.001s] +Building reference seed array... [0.008s] Building query seed array... [0s] -Computing hash join... [0s] +Computing hash join... [0.002s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.006s] 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 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 7/16, index chunk 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +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... [0.001s] 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... [0.004s] Building query seed array... [0s] 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 8/16, 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] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.004s] 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 reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.003s] 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... [0.003s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] @@ -12343,34 +12379,34 @@ 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... [0s] -Computing hash join... [0s] +Building query seed array... [0.006s] +Computing hash join... [0.003s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] 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... [0s] +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 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... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Computing hash join... [0.006s] +Masking low complexity seeds... [0.004s] +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... [0s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.004s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.002s] 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] @@ -12378,30 +12414,30 @@ 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... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.005s] +Masking low complexity seeds... [0.001s] +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... [0s] +Building reference seed array... [0.005s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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... [0.004s] 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 11/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building reference seed array... [0.004s] +Building query seed array... [0.001s] +Computing hash join... [0.004s] +Masking low complexity seeds... [0.003s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. @@ -12409,55 +12445,55 @@ Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.005s] 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... [0s] -Computing hash join... [0s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] -Computing hash join... [0s] +Building reference seed array... [0.006s] +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 12/16, index chunk 2/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +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 12/16, 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] +Searching alignments... [0.004s] 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... [0.007s] 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 1/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +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 13/16, 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] +Masking low complexity seeds... [0.002s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4. @@ -12465,102 +12501,102 @@ Building query seed array... [0s] 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 13/16, 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 14/16, 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... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4. -Building reference seed array... [0.002s] +Building reference seed array... [0.001s] Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.008s] 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... [0s] -Computing hash join... [0s] +Building reference seed array... [0.008s] +Building query seed array... [0.001s] +Computing hash join... [0.001s] Masking low complexity seeds... [0s] -Searching alignments... [0s] -Deallocating memory... [0s] +Searching alignments... [0.003s] +Deallocating memory... [0.001s] 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... [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] -Building query seed array... [0s] +Building reference seed array... [0.013s] +Building query seed array... [0.006s] 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 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 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] -Searching alignments... [0s] -Deallocating memory... [0s] +Masking low complexity seeds... [0.004s] +Searching alignments... [0.004s] +Deallocating memory... [0.001s] 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... [0s] +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 16/16, index chunk 2/4. -Building reference seed array... [0.001s] -Building query seed array... [0s] +Building reference seed array... [0.009s] +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 3/4. -Building reference seed array... [0.002s] -Building query seed array... [0s] +Building reference seed array... [0.004s] +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 16/16, index chunk 4/4. Building reference seed array... [0.001s] -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] Deallocating buffers... [0s] Clearing query masking... [0s] -Computing alignments... [0.006s] +Computing alignments... [0.026s] Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] @@ -12570,17 +12606,17 @@ Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.39s +Total time = 0.803s 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.6OycLsGn47/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.M86lnC5iOP/M.faa.vs.C2.faa.diamond -e 1e-05 --outfmt 6 --sensitive diamond v2.1.14.168 (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.6OycLsGn47 +Temporary directory: /tmp/tmp.M86lnC5iOP #Target sequences to report alignments for: 25 Opening the database... [0s] Database: test/C2.faa.diamond (type: Diamond database, sequences: 2, letters: 726) @@ -12588,9 +12624,9 @@ Opening the input file... [0s] Opening the output file... [0s] Loading query sequences... [0s] -Masking queries... [0.002s] +Masking queries... [0.001s] Algorithm: Double-indexed -Building query histograms... [0.013s] +Building query histograms... [0.009s] Seeking in database... [0s] Loading reference sequences... [0s] Masking reference... [0s] @@ -12599,51 +12635,51 @@ 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... [0.002s] +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 1/16, index chunk 2/4. -Building reference seed array... [0s] -Building query seed array... [0.001s] +Building reference seed array... [0.003s] +Building query seed array... [0.006s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0.001s] +Masking low complexity seeds... [0.002s] +Searching alignments... [0.004s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.002s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.003s] 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... [0.003s] 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 1/4. Building reference seed array... [0s] -Building query 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 2/16, index chunk 2/4. -Building reference seed array... [0s] -Building query 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... [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... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Building query seed array... [0s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.003s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4. @@ -12656,167 +12692,167 @@ Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4. Building reference seed array... [0s] Building query seed array... [0.001s] -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 3/16, 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] +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... [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... [0.002s] 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 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... [0s] -Building query seed array... [0.002s] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.005s] 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... [0.006s] +Building query seed array... [0.003s] 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 4/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +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 4/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.002s] +Building query seed array... [0s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.001s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 5/16, 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] +Masking low complexity seeds... [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... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.009s] +Building query seed array... [0.001s] 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 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] +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... [0.003s] -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] +Masking low complexity seeds... [0.007s] 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... [0.001s] -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] +Searching alignments... [0.002s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4. Building reference seed array... [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] +Searching alignments... [0.006s] 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... [0.001s] -Computing hash join... [0s] +Building reference seed array... [0.004s] +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 6/16, 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 7/16, 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 7/16, index chunk 2/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +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... [0s] -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] +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... [0s] -Building query seed array... [0.002s] +Building query seed array... [0.001s] 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 8/16, index chunk 1/4. Building reference seed array... [0s] -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 8/16, index chunk 2/4. -Building reference seed array... [0s] +Building reference seed array... [0.006s] Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.003s] 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... [0.007s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4. -Building reference seed array... [0s] -Building query seed array... [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] @@ -12825,42 +12861,42 @@ Building reference seed array... [0s] Building query seed array... [0.001s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.003s] 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 reference seed array... [0.001s] Building query seed array... [0.001s] -Computing hash join... [0s] +Computing hash join... [0.004s] 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... [0.001s] -Computing hash join... [0s] +Building query seed array... [0.004s] +Computing hash join... [0.003s] 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 4/4. -Building reference seed array... [0s] -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] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4. -Building reference seed array... [0s] +Building reference seed array... [0.001s] Building query seed array... [0.001s] -Computing hash join... [0s] +Computing hash join... [0.009s] 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... [0s] -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] +Masking low complexity seeds... [0.005s] Searching alignments... [0s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4. @@ -12879,56 +12915,56 @@ 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... [0.002s] +Building query seed array... [0.004s] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.003s] +Searching alignments... [0.006s] 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... [0.001s] +Building reference seed array... [0.002s] +Building query seed array... [0.006s] Computing hash join... [0s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.011s] Deallocating memory... [0s] Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4. -Building reference seed array... [0s] +Building reference seed array... [0.008s] Building query seed array... [0.002s] -Computing hash join... [0s] +Computing hash join... [0.002s] 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 4/4. -Building reference seed array... [0s] -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 1/4. -Building reference seed array... [0s] -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] +Masking low complexity seeds... [0.001s] +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... [0s] -Building query seed array... [0.001s] +Building reference seed array... [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 12/16, index chunk 3/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +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 12/16, index chunk 4/4. Building reference seed array... [0s] -Building query seed array... [0.001s] +Building query seed array... [0.004s] Computing hash join... [0s] Masking low complexity seeds... [0s] Searching alignments... [0s] @@ -12938,112 +12974,112 @@ 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 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] +Searching alignments... [0.002s] 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] -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 13/16, index chunk 4/4. -Building reference seed array... [0s] -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] +Searching alignments... [0.002s] 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 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 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] +Searching alignments... [0.002s] 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... [0.001s] -Building query seed array... [0.002s] +Building reference seed array... [0.003s] +Building query seed array... [0.006s] 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 15/16, index chunk 1/4. Building reference seed array... [0s] Building query seed array... [0.002s] -Computing hash join... [0s] -Masking low complexity seeds... [0s] +Computing hash join... [0.001s] +Masking low complexity seeds... [0.009s] 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... [0.006s] -Computing hash join... [0s] +Building query seed array... [0.001s] +Computing hash join... [0.005s] Masking low complexity seeds... [0s] -Searching alignments... [0s] +Searching alignments... [0.003s] 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] 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... [0s] -Building query seed array... [0.002s] +Building reference seed array... [0.001s] +Building query seed array... [0.011s] Computing hash join... [0s] -Masking low complexity seeds... [0s] +Masking low complexity seeds... [0.003s] Searching alignments... [0s] -Deallocating memory... [0s] +Deallocating memory... [0.004s] 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] +Searching alignments... [0.002s] 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] Computing hash join... [0s] -Masking low complexity seeds... [0s] -Searching alignments... [0s] +Masking low complexity seeds... [0.005s] +Searching alignments... [0.003s] Deallocating memory... [0s] Deallocating buffers... [0s] Clearing query masking... [0s] @@ -13051,16 +13087,16 @@ Deallocating reference... [0s] Loading reference sequences... [0s] Deallocating buffers... [0s] -Deallocating queries... [0s] +Deallocating queries... [0.001s] Loading query sequences... [0s] Closing the input file... [0s] Closing the output file... [0s] Closing the database... [0s] Cleaning up... [0s] -Total time = 0.48s +Total time = 0.715s Reported 1 pairwise alignments, 1 HSPs. 1 queries aligned. -+ rm -rf /tmp/tmp.6OycLsGn47 ++ rm -rf /tmp/tmp.M86lnC5iOP make[1]: Leaving directory '/build/reproducible-path/diamond-aligner-2.1.14' create-stamp debian/debhelper-build-stamp dh_prep @@ -13101,8 +13137,8 @@ dh_gencontrol dh_md5sums dh_builddeb -dpkg-deb: building package 'diamond-aligner' in '../diamond-aligner_2.1.14-1_arm64.deb'. dpkg-deb: building package 'diamond-aligner-dbgsym' in '../diamond-aligner-dbgsym_2.1.14-1_arm64.deb'. +dpkg-deb: building package 'diamond-aligner' in '../diamond-aligner_2.1.14-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../diamond-aligner_2.1.14-1_arm64.buildinfo dpkg-genchanges --build=binary -O../diamond-aligner_2.1.14-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -13110,12 +13146,14 @@ 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/2242308/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/2242308/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/1342373 and its subdirectories -I: Current time: Mon Oct 20 13:38:26 -12 2025 -I: pbuilder-time-stamp: 1761010706 +I: removing directory /srv/workspace/pbuilder/2242308 and its subdirectories +I: Current time: Mon Nov 23 22:10:07 +14 2026 +I: pbuilder-time-stamp: 1795421407